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docs/namespacescran_1_1crispr__quality__control.html create mode 100644 docs/structscran_1_1crispr__quality__control_1_1FiltersOptions-members.html create mode 100644 docs/structscran_1_1crispr__quality__control_1_1FiltersOptions.html create mode 100644 docs/structscran_1_1crispr__quality__control_1_1MetricsBuffers-members.html create mode 100644 docs/structscran_1_1crispr__quality__control_1_1MetricsBuffers.html create mode 100644 docs/structscran_1_1crispr__quality__control_1_1MetricsOptions-members.html create mode 100644 docs/structscran_1_1crispr__quality__control_1_1MetricsOptions.html create mode 100644 docs/structscran_1_1crispr__quality__control_1_1MetricsResults-members.html create mode 100644 docs/structscran_1_1crispr__quality__control_1_1MetricsResults.html diff --git a/docs/annotated.html b/docs/annotated.html index 2fe4b09..2bbe049 100644 --- a/docs/annotated.html +++ b/docs/annotated.html @@ -87,21 +87,28 @@  Nchoose_filter_thresholdsDefine QC filter thresholds using a MAD-based approach  COptionsOptions for compute()  CResultsResults of compute() - Nfind_median_madCalculate the median and MAD from an array of values - COptionsOptions for find_median_mad::compute() - CResultsContainer for the median and MAD - CWorkspaceTemporary data structures for compute_blocked() - Nper_cell_qc_metricsCompute per-cell quality control metrics - CBuffersBuffers for direct storage of the calculated statistics - COptionsOptions for compute() - CResultsResult store for QC metric calculations - Nrna_quality_controlSimple per-cell QC metrics from an RNA count matrix - CBlockedFiltersFilter for high-quality cells using RNA-based metrics with blocking - CFiltersFilter for high-quality cells using RNA-based metrics - CFiltersOptionsOptions for Filters() - CMetricsBuffersBuffers for direct storage of the calculated statistics - CMetricsOptionsOptions for compute_metrics() - CMetricsResultsResults of the QC metric calculations + Ncrispr_quality_controlSimple per-cell QC metrics from a CRISPR count matrix + CBlockedFiltersFilter for high-quality cells using CRISPR-based metrics with blocking + CFiltersFilter for high-quality cells using CRISPR-based metrics + CFiltersOptionsOptions for Filters() + CMetricsBuffersBuffers for direct storage of the calculated statistics + CMetricsOptionsOptions for compute_metrics() + CMetricsResultsResults of the QC metric calculations + Nfind_median_madCalculate the median and MAD from an array of values + COptionsOptions for find_median_mad::compute() + CResultsContainer for the median and MAD + CWorkspaceTemporary data structures for compute_blocked() + Nper_cell_qc_metricsCompute per-cell quality control metrics + CBuffersBuffers for direct storage of the calculated statistics + COptionsOptions for compute() + CResultsResult store for QC metric calculations + Nrna_quality_controlSimple per-cell QC metrics from an RNA count matrix + CBlockedFiltersFilter for high-quality cells using RNA-based metrics with blocking + CFiltersFilter for high-quality cells using RNA-based metrics + CFiltersOptionsOptions for Filters() + CMetricsBuffersBuffers for direct storage of the calculated statistics + CMetricsOptionsOptions for compute_metrics() + CMetricsResultsResults of the QC metric calculations diff --git a/docs/choose__filter__thresholds_8hpp.html b/docs/choose__filter__thresholds_8hpp.html index 035fcf1..8a651d9 100644 --- a/docs/choose__filter__thresholds_8hpp.html +++ b/docs/choose__filter__thresholds_8hpp.html @@ -119,11 +119,13 @@
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B
-
BlockedFilters (scran::adt_quality_control)
BlockedFilters (scran::rna_quality_control)
Buffers (scran::per_cell_qc_metrics)
+
BlockedFilters (scran::adt_quality_control)
BlockedFilters (scran::crispr_quality_control)
BlockedFilters (scran::rna_quality_control)
Buffers (scran::per_cell_qc_metrics)
F
-
Filters (scran::adt_quality_control)
Filters (scran::rna_quality_control)
FiltersOptions (scran::adt_quality_control)
FiltersOptions (scran::rna_quality_control)
+
Filters (scran::adt_quality_control)
Filters (scran::crispr_quality_control)
Filters (scran::rna_quality_control)
FiltersOptions (scran::adt_quality_control)
FiltersOptions (scran::crispr_quality_control)
FiltersOptions (scran::rna_quality_control)
M
-
MetricsBuffers (scran::adt_quality_control)
MetricsBuffers (scran::rna_quality_control)
MetricsOptions (scran::adt_quality_control)
MetricsOptions (scran::rna_quality_control)
MetricsResults (scran::adt_quality_control)
MetricsResults (scran::rna_quality_control)
+
MetricsBuffers (scran::adt_quality_control)
MetricsBuffers (scran::crispr_quality_control)
MetricsBuffers (scran::rna_quality_control)
MetricsOptions (scran::adt_quality_control)
MetricsOptions (scran::crispr_quality_control)
MetricsOptions (scran::rna_quality_control)
MetricsResults (scran::adt_quality_control)
MetricsResults (scran::crispr_quality_control)
MetricsResults (scran::rna_quality_control)
O
Options (scran::choose_filter_thresholds)
Options (scran::find_median_mad)
Options (scran::per_cell_qc_metrics)
diff --git a/docs/classscran_1_1crispr__quality__control_1_1BlockedFilters-members.html b/docs/classscran_1_1crispr__quality__control_1_1BlockedFilters-members.html new file mode 100644 index 0000000..fb08c91 --- /dev/null +++ b/docs/classscran_1_1crispr__quality__control_1_1BlockedFilters-members.html @@ -0,0 +1,96 @@ + + + + + + + +scran_quality_control: Member List + + + + + + + + + + +
+
+ + + + + + +
+
scran_quality_control +
+
Compute simple per-cell quality control metrics
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scran::crispr_quality_control::BlockedFilters< Float_ > Member List
+
+
+ +

This is the complete list of members for scran::crispr_quality_control::BlockedFilters< Float_ >, including all inherited members.

+ + + + + + + +
BlockedFilters()=defaultscran::crispr_quality_control::BlockedFilters< Float_ >
filter(size_t num, const MetricsBuffers< Sum_, Detected_, Value_, Index_ > &metrics, const Block_ *block, Output_ *output) constscran::crispr_quality_control::BlockedFilters< Float_ >inline
filter(const MetricsResults< Sum_, Detected_, Value_, Index_ > &metrics, const Block_ *block, Output_ *output) constscran::crispr_quality_control::BlockedFilters< Float_ >inline
filter(const MetricsResults< Sum_, Detected_, Value_, Index_ > &metrics, const Block_ *block) constscran::crispr_quality_control::BlockedFilters< Float_ >inline
get_max_value() constscran::crispr_quality_control::BlockedFilters< Float_ >inline
get_max_value()scran::crispr_quality_control::BlockedFilters< Float_ >inline
+ + + + diff --git a/docs/classscran_1_1crispr__quality__control_1_1BlockedFilters.html b/docs/classscran_1_1crispr__quality__control_1_1BlockedFilters.html new file mode 100644 index 0000000..c4ae159 --- /dev/null +++ b/docs/classscran_1_1crispr__quality__control_1_1BlockedFilters.html @@ -0,0 +1,408 @@ + + + + + + + +scran_quality_control: scran::crispr_quality_control::BlockedFilters< Float_ > Class Template Reference + + + + + + + + + + +
+
+ + + + + + +
+
scran_quality_control +
+
Compute simple per-cell quality control metrics
+
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scran::crispr_quality_control::BlockedFilters< Float_ > Class Template Reference
+
+
+ +

Filter for high-quality cells using CRISPR-based metrics with blocking. + More...

+ +

#include <crispr_quality_control.hpp>

+ + + + + + + + + + + + + + + + + +

+Public Member Functions

 BlockedFilters ()=default
 
const std::vector< Float_ > & get_max_value () const
 
std::vector< Float_ > & get_max_value ()
 
template<typename Sum_ , typename Detected_ , typename Value_ , typename Index_ , typename Block_ , typename Output_ >
void filter (size_t num, const MetricsBuffers< Sum_, Detected_, Value_, Index_ > &metrics, const Block_ *block, Output_ *output) const
 
template<typename Sum_ , typename Detected_ , typename Value_ , typename Index_ , typename Block_ , typename Output_ >
void filter (const MetricsResults< Sum_, Detected_, Value_, Index_ > &metrics, const Block_ *block, Output_ *output) const
 
template<typename Output_ = uint8_t, typename Sum_ = double, typename Detected_ = int, typename Value_ = double, typename Index_ = int, typename Block_ = int>
std::vector< Output_ > filter (const MetricsResults< Sum_, Detected_, Value_, Index_ > &metrics, const Block_ *block) const
 
+

Detailed Description

+
template<typename Float_ = double>
+class scran::crispr_quality_control::BlockedFilters< Float_ >

Filter for high-quality cells using CRISPR-based metrics with blocking.

+
Template Parameters
+ + +
Float_Floating-point type for filter thresholds.
+
+
+

Constructor & Destructor Documentation

+ +

◆ BlockedFilters()

+ +
+
+
+template<typename Float_ = double>
+ + + + + +
+ + + + + + + +
scran::crispr_quality_control::BlockedFilters< Float_ >::BlockedFilters ()
+
+default
+
+

Default constructor.

+ +
+
+

Member Function Documentation

+ +

◆ get_max_value() [1/2]

+ +
+
+
+template<typename Float_ = double>
+ + + + + +
+ + + + + + + +
const std::vector< Float_ > & scran::crispr_quality_control::BlockedFilters< Float_ >::get_max_value () const
+
+inline
+
+
Returns
Vector of length equal to the number of blocks, containing the lower threshold on the maximum count in each block.
+ +
+
+ +

◆ get_max_value() [2/2]

+ +
+
+
+template<typename Float_ = double>
+ + + + + +
+ + + + + + + +
std::vector< Float_ > & scran::crispr_quality_control::BlockedFilters< Float_ >::get_max_value ()
+
+inline
+
+
Returns
Vector of length equal to the number of blocks, containing the lower threshold on the maximum count in each block.
+ +
+
+ +

◆ filter() [1/3]

+ +
+
+
+template<typename Float_ = double>
+
+template<typename Sum_ , typename Detected_ , typename Value_ , typename Index_ , typename Block_ , typename Output_ >
+ + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
void scran::crispr_quality_control::BlockedFilters< Float_ >::filter (size_t num,
const MetricsBuffers< Sum_, Detected_, Value_, Index_ > & metrics,
const Block_ * block,
Output_ * output 
) const
+
+inline
+
+
Template Parameters
+ + + + + + + +
Sum_Numeric type to store the summed expression.
Detected_Integer type to store the number of cells.
Value_Type of matrix value.
Index_Type of the matrix indices.
Block_Integer type for the block assignment.
Output_Boolean type to store the high quality flags.
+
+
+
Parameters
+ + + + + +
numNumber of cells.
metricsA collection of arrays containing CRISPR-based QC metrics, filled by compute_metrics().
[in]blockPointer to an array of length num containing block identifiers. Each identifier should correspond to the same blocks used in the constructor.
[out]outputPointer to an array of length num. On output, this is truthy for cells considered to be of high quality, and false otherwise.
+
+
+ +
+
+ +

◆ filter() [2/3]

+ +
+
+
+template<typename Float_ = double>
+
+template<typename Sum_ , typename Detected_ , typename Value_ , typename Index_ , typename Block_ , typename Output_ >
+ + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + +
void scran::crispr_quality_control::BlockedFilters< Float_ >::filter (const MetricsResults< Sum_, Detected_, Value_, Index_ > & metrics,
const Block_ * block,
Output_ * output 
) const
+
+inline
+
+
Template Parameters
+ + + + + + + +
Sum_Numeric type to store the summed expression.
Detected_Integer type to store the number of cells.
Value_Type of matrix value.
Index_Type of the matrix indices.
Block_Integer type for the block assignment.
Output_Boolean type to store the high quality flags.
+
+
+
Parameters
+ + + + +
metricsCRISPR-based QC metrics computed by compute_metrics().
[in]blockPointer to an array of length num containing block identifiers. Each identifier should correspond to the same blocks used in the constructor.
[out]outputPointer to an array of length num. On output, this is truthy for cells considered to be of high quality, and false otherwise.
+
+
+ +
+
+ +

◆ filter() [3/3]

+ +
+
+
+template<typename Float_ = double>
+
+template<typename Output_ = uint8_t, typename Sum_ = double, typename Detected_ = int, typename Value_ = double, typename Index_ = int, typename Block_ = int>
+ + + + + +
+ + + + + + + + + + + + + + + + + + +
std::vector< Output_ > scran::crispr_quality_control::BlockedFilters< Float_ >::filter (const MetricsResults< Sum_, Detected_, Value_, Index_ > & metrics,
const Block_ * block 
) const
+
+inline
+
+
Template Parameters
+ + + + + + + +
Output_Boolean type to store the high quality flags.
Sum_Numeric type to store the summed expression.
Detected_Integer type to store the number of cells.
Value_Type of matrix value.
Index_Type of the matrix indices.
Block_Integer type for the block assignment.
+
+
+
Parameters
+ + + +
metricsCRISPR-based QC metrics computed by compute_metrics().
[in]blockPointer to an array of length num containing block identifiers. Each identifier should correspond to the same blocks used in the constructor.
+
+
+
Returns
Vector of length num, containing the high-quality calls.
+ +
+
+
The documentation for this class was generated from the following file: +
+ + + + diff --git a/docs/classscran_1_1crispr__quality__control_1_1Filters-members.html b/docs/classscran_1_1crispr__quality__control_1_1Filters-members.html new file mode 100644 index 0000000..5be6a0b --- /dev/null +++ b/docs/classscran_1_1crispr__quality__control_1_1Filters-members.html @@ -0,0 +1,96 @@ + + + + + + + +scran_quality_control: Member List + + + + + + + + + + +
+
+ + + + + + +
+
scran_quality_control +
+
Compute simple per-cell quality control metrics
+
+
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+
scran::crispr_quality_control::Filters< Float_ > Member List
+
+
+ +

This is the complete list of members for scran::crispr_quality_control::Filters< Float_ >, including all inherited members.

+ + + + + + + +
filter(size_t num, const MetricsBuffers< Sum_, Detected_, Value_, Index_ > &metrics, Output_ *output) constscran::crispr_quality_control::Filters< Float_ >inline
filter(const MetricsResults< Sum_, Detected_, Value_, Index_ > &metrics, Output_ *output) constscran::crispr_quality_control::Filters< Float_ >inline
filter(const MetricsResults< Sum_, Detected_, Value_, Index_ > &metrics) constscran::crispr_quality_control::Filters< Float_ >inline
Filters()=defaultscran::crispr_quality_control::Filters< Float_ >
get_max_value() constscran::crispr_quality_control::Filters< Float_ >inline
get_max_value()scran::crispr_quality_control::Filters< Float_ >inline
+ + + + diff --git a/docs/classscran_1_1crispr__quality__control_1_1Filters.html b/docs/classscran_1_1crispr__quality__control_1_1Filters.html new file mode 100644 index 0000000..c64af60 --- /dev/null +++ b/docs/classscran_1_1crispr__quality__control_1_1Filters.html @@ -0,0 +1,380 @@ + + + + + + + +scran_quality_control: scran::crispr_quality_control::Filters< Float_ > Class Template Reference + + + + + + + + + + +
+
+ + + + + + +
+
scran_quality_control +
+
Compute simple per-cell quality control metrics
+
+
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+
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scran::crispr_quality_control::Filters< Float_ > Class Template Reference
+
+
+ +

Filter for high-quality cells using CRISPR-based metrics. + More...

+ +

#include <crispr_quality_control.hpp>

+ + + + + + + + + + + + + + + + + +

+Public Member Functions

 Filters ()=default
 
Float_ get_max_value () const
 
Float_ & get_max_value ()
 
template<typename Sum_ , typename Detected_ , typename Value_ , typename Index_ , typename Output_ >
void filter (size_t num, const MetricsBuffers< Sum_, Detected_, Value_, Index_ > &metrics, Output_ *output) const
 
template<typename Sum_ , typename Detected_ , typename Value_ , typename Index_ , typename Output_ >
void filter (const MetricsResults< Sum_, Detected_, Value_, Index_ > &metrics, Output_ *output) const
 
template<typename Output_ = uint8_t, typename Sum_ = double, typename Detected_ = int, typename Value_ = double, typename Index_ = int>
std::vector< Output_ > filter (const MetricsResults< Sum_, Detected_, Value_, Index_ > &metrics) const
 
+

Detailed Description

+
template<typename Float_ = double>
+class scran::crispr_quality_control::Filters< Float_ >

Filter for high-quality cells using CRISPR-based metrics.

+
Template Parameters
+ + +
Float_Floating-point type for filter thresholds.
+
+
+

Constructor & Destructor Documentation

+ +

◆ Filters()

+ +
+
+
+template<typename Float_ = double>
+ + + + + +
+ + + + + + + +
scran::crispr_quality_control::Filters< Float_ >::Filters ()
+
+default
+
+

Default constructor.

+ +
+
+

Member Function Documentation

+ +

◆ get_max_value() [1/2]

+ +
+
+
+template<typename Float_ = double>
+ + + + + +
+ + + + + + + +
Float_ scran::crispr_quality_control::Filters< Float_ >::get_max_value () const
+
+inline
+
+
Returns
Lower threshold to apply to the maximum count.
+ +
+
+ +

◆ get_max_value() [2/2]

+ +
+
+
+template<typename Float_ = double>
+ + + + + +
+ + + + + + + +
Float_ & scran::crispr_quality_control::Filters< Float_ >::get_max_value ()
+
+inline
+
+
Returns
Lower threshold to apply to the maximum count.
+ +
+
+ +

◆ filter() [1/3]

+ +
+
+
+template<typename Float_ = double>
+
+template<typename Sum_ , typename Detected_ , typename Value_ , typename Index_ , typename Output_ >
+ + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + +
void scran::crispr_quality_control::Filters< Float_ >::filter (size_t num,
const MetricsBuffers< Sum_, Detected_, Value_, Index_ > & metrics,
Output_ * output 
) const
+
+inline
+
+
Template Parameters
+ + + + + + +
Sum_Numeric type to store the summed expression.
Detected_Integer type to store the number of cells.
Value_Type of matrix value.
Index_Type of the matrix indices.
Output_Boolean type to store the high quality flags.
+
+
+
Parameters
+ + + + +
numNumber of cells.
metricsA collection of arrays containing CRISPR-based QC metrics, filled by compute_metrics().
[out]outputPointer to an array of length num. On output, this is truthy for cells considered to be of high quality, and false otherwise.
+
+
+ +
+
+ +

◆ filter() [2/3]

+ +
+
+
+template<typename Float_ = double>
+
+template<typename Sum_ , typename Detected_ , typename Value_ , typename Index_ , typename Output_ >
+ + + + + +
+ + + + + + + + + + + + + + + + + + +
void scran::crispr_quality_control::Filters< Float_ >::filter (const MetricsResults< Sum_, Detected_, Value_, Index_ > & metrics,
Output_ * output 
) const
+
+inline
+
+
Template Parameters
+ + + + + + +
Sum_Numeric type to store the summed expression.
Detected_Integer type to store the number of cells.
Value_Type of matrix value.
Index_Type of the matrix indices.
Output_Boolean type to store the high quality flags.
+
+
+
Parameters
+ + + +
metricsCRISPR-based QC metrics returned by compute_metrics().
[out]outputPointer to an array of length num. On output, this is truthy for cells considered to be of high quality, and false otherwise.
+
+
+ +
+
+ +

◆ filter() [3/3]

+ +
+
+
+template<typename Float_ = double>
+
+template<typename Output_ = uint8_t, typename Sum_ = double, typename Detected_ = int, typename Value_ = double, typename Index_ = int>
+ + + + + +
+ + + + + + + + +
std::vector< Output_ > scran::crispr_quality_control::Filters< Float_ >::filter (const MetricsResults< Sum_, Detected_, Value_, Index_ > & metrics) const
+
+inline
+
+
Template Parameters
+ + + + + + +
Output_Boolean type to store the high quality flags.
Sum_Numeric type to store the summed expression.
Detected_Integer type to store the number of cells.
Value_Type of matrix value.
Index_Type of the matrix indices.
+
+
+
Parameters
+ + +
metricsCRISPR-based QC metrics returned by compute_metrics().
+
+
+
Returns
Vector of length num, containing the high-quality calls.
+ +
+
+
The documentation for this class was generated from the following file: +
+ + + + diff --git a/docs/crispr__quality__control_8hpp.html b/docs/crispr__quality__control_8hpp.html new file mode 100644 index 0000000..d0379b4 --- /dev/null +++ b/docs/crispr__quality__control_8hpp.html @@ -0,0 +1,201 @@ + + + + + + + +scran_quality_control: scran/crispr_quality_control.hpp File Reference + + + + + + + + + + +
+
+ + + + + + +
+
scran_quality_control +
+
Compute simple per-cell quality control metrics
+
+
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+ +
crispr_quality_control.hpp File Reference
+
+
+ +

Simple per-cell QC metrics from a CRISPR count matrix. +More...

+
#include <vector>
+#include <limits>
+#include <algorithm>
+#include <type_traits>
+#include "tatami/tatami.hpp"
+#include "find_median_mad.hpp"
+#include "per_cell_qc_metrics.hpp"
+#include "choose_filter_thresholds.hpp"
+
+Include dependency graph for crispr_quality_control.hpp:
+
+
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+
+

Go to the source code of this file.

+ + + + + + + + + + + + + + + + + + + + +

+Classes

struct  scran::crispr_quality_control::MetricsOptions
 Options for compute_metrics(). More...
 
struct  scran::crispr_quality_control::MetricsBuffers< Sum_, Detected_, Value_, Index_ >
 Buffers for direct storage of the calculated statistics. More...
 
struct  scran::crispr_quality_control::MetricsResults< Sum_, Detected_, Value_, Index_ >
 Results of the QC metric calculations. More...
 
struct  scran::crispr_quality_control::FiltersOptions
 Options for Filters(). More...
 
class  scran::crispr_quality_control::Filters< Float_ >
 Filter for high-quality cells using CRISPR-based metrics. More...
 
class  scran::crispr_quality_control::BlockedFilters< Float_ >
 Filter for high-quality cells using CRISPR-based metrics with blocking. More...
 
+ + + + + + + +

+Namespaces

namespace  scran
 Methods for single-cell analysis.
 
namespace  scran::crispr_quality_control
 Simple per-cell QC metrics from a CRISPR count matrix.
 
+ + + + + + + + + + + + + + + + + + + +

+Functions

template<typename Value_ , typename Index_ , typename Sum_ , typename Detected_ >
void scran::crispr_quality_control::compute_metrics (const tatami::Matrix< Value_, Index_ > *mat, MetricsBuffers< Sum_, Detected_, Value_, Index_ > &output, const MetricsOptions &options)
 
template<typename Sum_ = double, typename Detected_ = int, typename Value_ = double, typename Index_ = int>
MetricsResults< Sum_, Detected_, Value_, Index_ > scran::crispr_quality_control::compute_metrics (const tatami::Matrix< Value_, Index_ > *mat, const MetricsOptions &options)
 
template<typename Float_ = double, typename Sum_ = double, typename Detected_ = int, typename Value_ = double, typename Index_ = int>
Filters< Float_ > scran::crispr_quality_control::compute_filters (size_t num, const MetricsBuffers< Sum_, Detected_, Value_, Index_ > &metrics, const FiltersOptions &options)
 
template<typename Float_ = double, typename Sum_ = double, typename Detected_ = int, typename Value_ = double, typename Index_ = int>
Filters< Float_ > scran::crispr_quality_control::compute_filters (const MetricsResults< Sum_, Detected_, Value_, Index_ > &metrics, const FiltersOptions &options)
 
template<typename Float_ = double, typename Sum_ = double, typename Detected_ = int, typename Value_ = double, typename Index_ = int, typename Block_ = int>
BlockedFilters< Float_ > scran::crispr_quality_control::compute_filters_blocked (size_t num, const MetricsBuffers< Sum_, Detected_, Value_, Index_ > &metrics, const Block_ *block, const FiltersOptions &options)
 
template<typename Float_ = double, typename Sum_ = double, typename Detected_ = int, typename Value_ = double, typename Index_ = int, typename Block_ = int>
BlockedFilters< Float_ > scran::crispr_quality_control::compute_filters_blocked (const MetricsResults< Sum_, Detected_, Value_, Index_ > &metrics, const Block_ *block, const FiltersOptions &options)
 
+

Detailed Description

+

Simple per-cell QC metrics from a CRISPR count matrix.

+
+ + + + diff --git a/docs/crispr__quality__control_8hpp__incl.map b/docs/crispr__quality__control_8hpp__incl.map new file mode 100644 index 0000000..4ea6468 --- /dev/null +++ b/docs/crispr__quality__control_8hpp__incl.map @@ -0,0 +1,38 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/docs/crispr__quality__control_8hpp__incl.md5 b/docs/crispr__quality__control_8hpp__incl.md5 new file mode 100644 index 0000000..fa1d606 --- /dev/null +++ b/docs/crispr__quality__control_8hpp__incl.md5 @@ -0,0 +1 @@ +eddc95a16d3c46fc2ef1e65a4ea4949f \ No newline at end of file diff --git a/docs/crispr__quality__control_8hpp__incl.png b/docs/crispr__quality__control_8hpp__incl.png new file mode 100644 index 0000000000000000000000000000000000000000..4e977f529a0f5fe520be5d2e0df8421b3a1af308 GIT binary patch literal 58167 zcma&O1yt1Gw>C;iH_{E#-5nw!okORTqytDw3P^`YgM>&+NJ$C|QUe0g-6e>$G~RbS z|8v&)?ziq*R~I;r%*_7ncgM5$?|F>T(Ne*~rou)-Lc&vhs;GyAgi4KsgiMc#4xZr{ 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z$i4E3PK!S_8Kq&95nEwTEeD%YPX?K4hYD}o=7&sQ-y`mkXs{W-8@*H?|NiUCfvvff z=p*^6ko>iI^zS!?e_STJdo~X-qv#PrXCfQ4b~Q&II$**-Kd-OS{@E|5s^Z5-= m{Uh|A2cE!^_ + + + + + + +scran_quality_control: scran/crispr_quality_control.hpp Source File + + + + + + + + + + +

+
+ + + + + + +
+
scran_quality_control +
+
Compute simple per-cell quality control metrics
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+
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crispr_quality_control.hpp
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1#ifndef SCRAN_CRISPR_QUALITY_CONTROL_HPP
+
2#define SCRAN_CRISPR_QUALITY_CONTROL_HPP
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3
+
4#include <vector>
+
5#include <limits>
+
6#include <algorithm>
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7#include <type_traits>
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8
+
9#include "tatami/tatami.hpp"
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10
+
11#include "find_median_mad.hpp"
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14
+
21namespace scran {
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22
+
61namespace crispr_quality_control {
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62
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+ +
70 int num_threads = 1;
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71};
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+
72
+
80template<typename Sum_ = double, typename Detected_ = int, typename Value_ = double, typename Index_ = int>
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+ +
86 Sum_* sum = NULL;
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87
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92 Detected_* detected = NULL;
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93
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98 Value_* max_value = NULL;
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99
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104 Index_* max_index = NULL;
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105};
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106
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120template<typename Value_, typename Index_, typename Sum_, typename Detected_>
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+ + +
123 tmp.sum = output.sum;
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124 tmp.detected = output.detected;
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125 tmp.max_value = output.max_value;
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126 tmp.max_index = output.max_index;
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127
+ +
129 opt.num_threads = options.num_threads;
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130 per_cell_qc_metrics::compute(mat, std::vector<uint8_t*>{}, tmp, opt);
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131}
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+
132
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142template<typename Sum_ = double, typename Detected_ = int, typename Value_ = double, typename Index_ = int>
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+ +
147 MetricsResults() = default;
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155 std::vector<Sum_> sum;
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156
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160 std::vector<Detected_> detected;
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161
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165 std::vector<Value_> max_value;
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166
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170 std::vector<Index_> max_index;
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171};
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172
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189template<typename Sum_ = double, typename Detected_ = int, typename Value_ = double, typename Index_ = int>
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+ +
191 auto NC = mat->ncol();
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194
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195 output.sum.resize(NC);
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196 x.sum = output.sum.data();
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197
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198 output.detected.resize(NC);
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199 x.detected = output.detected.data();
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200
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201 output.max_value.resize(NC);
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202 x.max_value = output.max_value.data();
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203
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204 output.max_index.resize(NC);
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205 x.max_index = output.max_index.data();
+
206
+
207 compute_metrics(mat, x, options);
+
208 return output;
+
209}
+
+
210
+
+ + +
220};
+
+
221
+
225namespace internal {
+
226
+
227template<typename Float_, class Host_, typename Sum_, typename Detected_, typename Value_, typename Index_, typename BlockSource_>
+
228void populate(Host_& host, size_t n, const MetricsBuffers<Sum_, Detected_, Value_, Index_>& res, BlockSource_ block, const FiltersOptions& options) {
+
229 constexpr bool unblocked = std::is_same<BlockSource_, bool>::value;
+
230 auto buffer = [&]() {
+
231 if constexpr(unblocked) {
+
232 return std::vector<Float_>(n);
+
233 } else {
+ +
235 }
+
236 }();
+
237
+
238 // Subsetting to the observations in the top 50% of proportions.
+
239 static_assert(std::is_floating_point<Float_>::value);
+
240 std::vector<Float_> maxprop;
+
241 maxprop.reserve(n);
+
242 for (size_t i = 0; i < n; ++i) {
+
243 maxprop.push_back(static_cast<Float_>(res.max_value[i]) / static_cast<Float_>(res.sum[i]));
+
244 }
+
245
+ +
247 fopt.median_only = true;
+
248 auto prop_res = [&]() {
+
249 if constexpr(unblocked) {
+
250 return find_median_mad::compute(n, maxprop.data(), buffer.data(), fopt);
+
251 } else {
+
252 return find_median_mad::compute_blocked(n, maxprop.data(), block, &buffer, fopt);
+
253 }
+
254 }();
+
255
+
256 for (size_t i = 0; i < n; ++i) {
+
257 auto limit = [&]() {
+
258 if constexpr(unblocked){
+
259 return prop_res.median;
+
260 } else {
+
261 return prop_res[block[i]].median;
+
262 }
+
263 }();
+
264 if (maxprop[i] >= limit) {
+
265 maxprop[i] = res.max_value[i];
+
266 } else {
+
267 maxprop[i] = std::numeric_limits<Float_>::quiet_NaN(); // ignored during threshold calculation.
+
268 }
+
269 }
+
270
+
271 // Filtering on the max counts.
+ +
273 copt.num_mads = options.max_value_num_mads;
+
274 copt.log = true;
+
275 copt.upper = false;
+
276 host.get_max_value() = [&]() {
+
277 if constexpr(unblocked) {
+
278 return choose_filter_thresholds::compute(n, maxprop.data(), buffer.data(), copt).lower;
+
279 } else {
+
280 return choose_filter_thresholds::internal::strip<true>(choose_filter_thresholds::compute_blocked(n, maxprop.data(), block, &buffer, copt));
+
281 }
+
282 }();
+
283}
+
284
+
285template<class Host_, typename Sum_, typename Detected_, typename Value_, typename Index_, typename BlockSource_, typename Output_>
+
286void filter(const Host_& host, size_t n, const MetricsBuffers<Sum_, Detected_, Value_, Index_>& metrics, BlockSource_ block, Output_* output) {
+
287 constexpr bool unblocked = std::is_same<BlockSource_, bool>::value;
+
288 std::fill_n(output, n, 1);
+
289
+
290 for (size_t i = 0; i < n; ++i) {
+
291 auto thresh = [&]() {
+
292 if constexpr(unblocked) {
+
293 return host.get_max_value();
+
294 } else {
+
295 return host.get_max_value()[block[i]];
+
296 }
+
297 }();
+
298 output[i] = output[i] && (metrics.max_value[i] >= thresh);
+
299 }
+
300}
+
301
+
302template<typename Sum_, typename Detected_, typename Value_, typename Index_>
+
303MetricsBuffers<const Sum_, const Detected_, const Value_, const Index_> to_buffer(const MetricsResults<Sum_, Detected_, Value_, Index_>& metrics) {
+
304 MetricsBuffers<const Sum_, const Detected_, const Value_, const Index_> buffer;
+
305 buffer.sum = metrics.sum.data();
+
306 buffer.detected = metrics.detected.data();
+
307 buffer.max_value = metrics.max_value.data();
+
308 buffer.max_index = metrics.max_index.data();
+
309 return buffer;
+
310}
+
311
+
312}
+
321template<typename Float_ = double>
+
+
322class Filters {
+
323public:
+
327 Filters() = default;
+
328
+
329public:
+
+
333 Float_ get_max_value() const {
+
334 return my_max_value;
+
335 }
+
+
336
+
+
340 Float_& get_max_value() {
+
341 return my_max_value;
+
342 }
+
+
343
+
344private:
+
345 Float_ my_max_value = 0;
+
346
+
347public:
+
360 template<typename Sum_, typename Detected_, typename Value_, typename Index_, typename Output_>
+
+
361 void filter(size_t num, const MetricsBuffers<Sum_, Detected_, Value_, Index_>& metrics, Output_* output) const {
+
362 internal::filter(*this, num, metrics, false, output);
+
363 }
+
+
364
+
376 template<typename Sum_, typename Detected_, typename Value_, typename Index_, typename Output_>
+
+
377 void filter(const MetricsResults<Sum_, Detected_, Value_, Index_>& metrics, Output_* output) const {
+
378 return filter(metrics.max_value.size(), internal::to_buffer(metrics), output);
+
379 }
+
+
380
+
391 template<typename Output_ = uint8_t, typename Sum_ = double, typename Detected_ = int, typename Value_ = double, typename Index_ = int>
+
+
392 std::vector<Output_> filter(const MetricsResults<Sum_, Detected_, Value_, Index_>& metrics) const {
+
393 std::vector<Output_> output(metrics.max_value.size());
+
394 filter(metrics, output.data());
+
395 return output;
+
396 }
+
+
397};
+
+
398
+
413template<typename Float_ = double, typename Sum_ = double, typename Detected_ = int, typename Value_ = double, typename Index_ = int>
+
+ +
415 Filters<Float_> output;
+
416 internal::populate<Float_>(output, num, metrics, false, options);
+
417 return output;
+
418}
+
+
419
+
433template<typename Float_ = double, typename Sum_ = double, typename Detected_ = int, typename Value_ = double, typename Index_ = int>
+
+ +
435 return compute_filters(metrics.max_value.size(), internal::to_buffer(metrics), options);
+
436}
+
+
437
+
442template<typename Float_ = double>
+
+ +
444public:
+
448 BlockedFilters() = default;
+
449
+
450public:
+
+
455 const std::vector<Float_>& get_max_value() const {
+
456 return my_max_value;
+
457 }
+
+
458
+
+
463 std::vector<Float_>& get_max_value() {
+
464 return my_max_value;
+
465 }
+
+
466
+
467private:
+
468 std::vector<Float_> my_sum;
+
469 std::vector<Float_> my_max_value;
+
470 std::vector<std::vector<Float_> > my_subset_sum;
+
471
+
472public:
+
488 template<typename Sum_, typename Detected_, typename Value_, typename Index_, typename Block_, typename Output_>
+
+
489 void filter(size_t num, const MetricsBuffers<Sum_, Detected_, Value_, Index_>& metrics, const Block_* block, Output_* output) const {
+
490 internal::filter(*this, num, metrics, block, output);
+
491 }
+
+
492
+
507 template<typename Sum_, typename Detected_, typename Value_, typename Index_, typename Block_, typename Output_>
+
+
508 void filter(const MetricsResults<Sum_, Detected_, Value_, Index_>& metrics, const Block_* block, Output_* output) const {
+
509 filter(metrics.max_value.size(), internal::to_buffer(metrics), block, output);
+
510 }
+
+
511
+
526 template<typename Output_ = uint8_t, typename Sum_ = double, typename Detected_ = int, typename Value_ = double, typename Index_ = int, typename Block_ = int>
+
+
527 std::vector<Output_> filter(const MetricsResults<Sum_, Detected_, Value_, Index_>& metrics, const Block_* block) const {
+
528 std::vector<Output_> output(metrics.max_value.size());
+
529 filter(metrics, block, output.data());
+
530 return output;
+
531 }
+
+
532};
+
+
533
+
549template<typename Float_ = double, typename Sum_ = double, typename Detected_ = int, typename Value_ = double, typename Index_ = int, typename Block_ = int>
+
+ + +
552 internal::populate<Float_>(output, num, metrics, block, options);
+
553 return output;
+
554}
+
+
555
+
570template<typename Float_ = double, typename Sum_ = double, typename Detected_ = int, typename Value_ = double, typename Index_ = int, typename Block_ = int>
+
+ +
572 return compute_filters_blocked(metrics.max_value.size(), internal::to_buffer(metrics), block, options);
+
573}
+
+
574
+
575}
+
576
+
577}
+
578
+
579#endif
+
Define QC filter thresholds using a MAD-based approach.
+
Filter for high-quality cells using CRISPR-based metrics with blocking.
Definition crispr_quality_control.hpp:443
+
std::vector< Float_ > & get_max_value()
Definition crispr_quality_control.hpp:463
+ +
const std::vector< Float_ > & get_max_value() const
Definition crispr_quality_control.hpp:455
+
std::vector< Output_ > filter(const MetricsResults< Sum_, Detected_, Value_, Index_ > &metrics, const Block_ *block) const
Definition crispr_quality_control.hpp:527
+
void filter(const MetricsResults< Sum_, Detected_, Value_, Index_ > &metrics, const Block_ *block, Output_ *output) const
Definition crispr_quality_control.hpp:508
+
void filter(size_t num, const MetricsBuffers< Sum_, Detected_, Value_, Index_ > &metrics, const Block_ *block, Output_ *output) const
Definition crispr_quality_control.hpp:489
+
Filter for high-quality cells using CRISPR-based metrics.
Definition crispr_quality_control.hpp:322
+
Float_ get_max_value() const
Definition crispr_quality_control.hpp:333
+
void filter(const MetricsResults< Sum_, Detected_, Value_, Index_ > &metrics, Output_ *output) const
Definition crispr_quality_control.hpp:377
+
Float_ & get_max_value()
Definition crispr_quality_control.hpp:340
+ +
std::vector< Output_ > filter(const MetricsResults< Sum_, Detected_, Value_, Index_ > &metrics) const
Definition crispr_quality_control.hpp:392
+
void filter(size_t num, const MetricsBuffers< Sum_, Detected_, Value_, Index_ > &metrics, Output_ *output) const
Definition crispr_quality_control.hpp:361
+
Temporary data structures for compute_blocked().
Definition find_median_mad.hpp:177
+ +
virtual Index_ ncol() const=0
+
Compute the median and MAD from an array of values.
+
Filters< Float_ > compute_filters(size_t num, const MetricsBuffers< Sum_, Detected_, Value_, Index_ > &metrics, const FiltersOptions &options)
Definition crispr_quality_control.hpp:414
+
BlockedFilters< Float_ > compute_filters_blocked(size_t num, const MetricsBuffers< Sum_, Detected_, Value_, Index_ > &metrics, const Block_ *block, const FiltersOptions &options)
Definition crispr_quality_control.hpp:550
+
void compute_metrics(const tatami::Matrix< Value_, Index_ > *mat, MetricsBuffers< Sum_, Detected_, Value_, Index_ > &output, const MetricsOptions &options)
Definition crispr_quality_control.hpp:121
+
void compute(const tatami::Matrix< Value_, Index_ > *mat, const std::vector< Subset_ > &subsets, Buffers< Sum_, Detected_, Value_, Index_ > &output, const Options &options)
Definition per_cell_qc_metrics.hpp:794
+
Methods for single-cell analysis.
Definition adt_quality_control.hpp:21
+
Compute per-cell quality control metrics.
+
Options for compute().
Definition choose_filter_thresholds.hpp:37
+
bool log
Definition choose_filter_thresholds.hpp:68
+
bool upper
Definition choose_filter_thresholds.hpp:48
+
double num_mads
Definition choose_filter_thresholds.hpp:55
+
Options for Filters().
Definition crispr_quality_control.hpp:214
+
double max_value_num_mads
Definition crispr_quality_control.hpp:219
+
Buffers for direct storage of the calculated statistics.
Definition crispr_quality_control.hpp:81
+
Index_ * max_index
Definition crispr_quality_control.hpp:104
+
Sum_ * sum
Definition crispr_quality_control.hpp:86
+
Value_ * max_value
Definition crispr_quality_control.hpp:98
+
Detected_ * detected
Definition crispr_quality_control.hpp:92
+
Options for compute_metrics().
Definition crispr_quality_control.hpp:66
+
int num_threads
Definition crispr_quality_control.hpp:70
+
Results of the QC metric calculations.
Definition crispr_quality_control.hpp:143
+
std::vector< Index_ > max_index
Definition crispr_quality_control.hpp:170
+
std::vector< Detected_ > detected
Definition crispr_quality_control.hpp:160
+
std::vector< Value_ > max_value
Definition crispr_quality_control.hpp:165
+
std::vector< Sum_ > sum
Definition crispr_quality_control.hpp:155
+
Options for find_median_mad::compute().
Definition find_median_mad.hpp:32
+
bool median_only
Definition find_median_mad.hpp:44
+
Buffers for direct storage of the calculated statistics.
Definition per_cell_qc_metrics.hpp:98
+
Detected_ * detected
Definition per_cell_qc_metrics.hpp:119
+
Index_ * max_index
Definition per_cell_qc_metrics.hpp:125
+
Sum_ * sum
Definition per_cell_qc_metrics.hpp:113
+
Value_ * max_value
Definition per_cell_qc_metrics.hpp:131
+
Options for compute().
Definition per_cell_qc_metrics.hpp:46
+
int num_threads
Definition per_cell_qc_metrics.hpp:86
+ +
+ + + + diff --git a/docs/dir_bdabb9492db2368b3caf0f4c1df6a160.html b/docs/dir_bdabb9492db2368b3caf0f4c1df6a160.html index 3e7d762..970bcbb 100644 --- a/docs/dir_bdabb9492db2368b3caf0f4c1df6a160.html +++ b/docs/dir_bdabb9492db2368b3caf0f4c1df6a160.html @@ -87,6 +87,9 @@  choose_filter_thresholds.hpp  Define QC filter thresholds using a MAD-based approach.
  + crispr_quality_control.hpp + Simple per-cell QC metrics from a CRISPR count matrix.
 find_median_mad.hpp  Compute the median and MAD from an array of values.
  diff --git a/docs/files.html b/docs/files.html index 1a5dc59..a496803 100644 --- a/docs/files.html +++ b/docs/files.html @@ -79,10 +79,11 @@   scran  adt_quality_control.hppSimple per-cell QC metrics from an ADT count matrix  choose_filter_thresholds.hppDefine QC filter thresholds using a MAD-based approach - find_median_mad.hppCompute the median and MAD from an array of values - per_cell_qc_metrics.hppCompute per-cell quality control metrics - rna_quality_control.hppSimple per-cell QC metrics from an RNA count matrix - scran.hppMethods for single-cell analysis + crispr_quality_control.hppSimple per-cell QC metrics from a CRISPR count matrix + find_median_mad.hppCompute the median and MAD from an array of values + per_cell_qc_metrics.hppCompute per-cell quality control metrics + rna_quality_control.hppSimple per-cell QC metrics from an RNA count matrix + scran.hppMethods for single-cell analysis
diff --git a/docs/find__median__mad_8hpp.html b/docs/find__median__mad_8hpp.html index 1322da1..c541e46 100644 --- a/docs/find__median__mad_8hpp.html +++ b/docs/find__median__mad_8hpp.html @@ -116,15 +116,18 @@
- - - - - - - - - + + + + + + + + + + + +
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a/docs/functions.html +++ b/docs/functions.html @@ -74,7 +74,7 @@
Here is a list of all documented class members with links to the class documentation for each member:

- b -

@@ -89,21 +89,22 @@

- c -

    - d -

    - f -

    - g -

    @@ -117,8 +118,9 @@

    - l -

      - m -

      • mad : scran::find_median_mad::Results< Float_ >
      • -
      • max_index : scran::per_cell_qc_metrics::Buffers< Sum_, Detected_, Value_, Index_ >, scran::per_cell_qc_metrics::Results< Sum_, Detected_, Value_, Index_ >
      • -
      • max_value : scran::per_cell_qc_metrics::Buffers< Sum_, Detected_, Value_, Index_ >, scran::per_cell_qc_metrics::Results< Sum_, Detected_, Value_, Index_ >
      • +
      • max_index : scran::crispr_quality_control::MetricsBuffers< Sum_, Detected_, Value_, Index_ >, scran::crispr_quality_control::MetricsResults< Sum_, Detected_, Value_, Index_ >, scran::per_cell_qc_metrics::Buffers< Sum_, Detected_, Value_, Index_ >, scran::per_cell_qc_metrics::Results< Sum_, Detected_, Value_, Index_ >
      • +
      • max_value : scran::crispr_quality_control::MetricsBuffers< Sum_, Detected_, Value_, Index_ >, scran::crispr_quality_control::MetricsResults< Sum_, Detected_, Value_, Index_ >, scran::per_cell_qc_metrics::Buffers< Sum_, Detected_, Value_, Index_ >, scran::per_cell_qc_metrics::Results< Sum_, Detected_, Value_, Index_ >
      • +
      • max_value_num_mads : scran::crispr_quality_control::FiltersOptions
      • median : scran::find_median_mad::Results< Float_ >
      • median_only : scran::find_median_mad::Options
      • min_diff : scran::choose_filter_thresholds::Options
      • @@ -127,7 +129,7 @@

        - m -

          - n -

          @@ -138,7 +140,7 @@

          - s -

          diff --git a/docs/functions_func.html b/docs/functions_func.html index 238d973..fe07841 100644 --- a/docs/functions_func.html +++ b/docs/functions_func.html @@ -74,19 +74,20 @@
          Here is a list of all documented functions with links to the class documentation for each member:

          - b -

          - f -

          - g -

          diff --git a/docs/functions_vars.html b/docs/functions_vars.html index 50bc750..f1672bb 100644 --- a/docs/functions_vars.html +++ b/docs/functions_vars.html @@ -84,7 +84,7 @@

          - c -

            - d -

            @@ -98,8 +98,9 @@

            - l -

              - m -

              • mad : scran::find_median_mad::Results< Float_ >
              • -
              • max_index : scran::per_cell_qc_metrics::Buffers< Sum_, Detected_, Value_, Index_ >, scran::per_cell_qc_metrics::Results< Sum_, Detected_, Value_, Index_ >
              • -
              • max_value : scran::per_cell_qc_metrics::Buffers< Sum_, Detected_, Value_, Index_ >, scran::per_cell_qc_metrics::Results< Sum_, Detected_, Value_, Index_ >
              • +
              • max_index : scran::crispr_quality_control::MetricsBuffers< Sum_, Detected_, Value_, Index_ >, scran::crispr_quality_control::MetricsResults< Sum_, Detected_, Value_, Index_ >, scran::per_cell_qc_metrics::Buffers< Sum_, Detected_, Value_, Index_ >, scran::per_cell_qc_metrics::Results< Sum_, Detected_, Value_, Index_ >
              • +
              • max_value : scran::crispr_quality_control::MetricsBuffers< Sum_, Detected_, Value_, Index_ >, scran::crispr_quality_control::MetricsResults< Sum_, Detected_, Value_, Index_ >, scran::per_cell_qc_metrics::Buffers< Sum_, Detected_, Value_, Index_ >, scran::per_cell_qc_metrics::Results< Sum_, Detected_, Value_, Index_ >
              • +
              • max_value_num_mads : scran::crispr_quality_control::FiltersOptions
              • median : scran::find_median_mad::Results< Float_ >
              • median_only : scran::find_median_mad::Options
              • min_diff : scran::choose_filter_thresholds::Options
              • @@ -108,7 +109,7 @@

                - m -

                  - n -

                  @@ -118,7 +119,7 @@

                  - s -

                  diff --git a/docs/namespacemembers.html b/docs/namespacemembers.html index 1c4dc26..6a75a2b 100644 --- a/docs/namespacemembers.html +++ b/docs/namespacemembers.html @@ -74,9 +74,9 @@
                  Here is a list of all documented namespace members with links to the namespaces they belong to:
                  diff --git a/docs/namespacemembers_func.html b/docs/namespacemembers_func.html index 0848c70..754323b 100644 --- a/docs/namespacemembers_func.html +++ b/docs/namespacemembers_func.html @@ -74,9 +74,9 @@
                  Here is a list of all documented namespace functions with links to the namespaces they belong to:
                  diff --git a/docs/namespaces.html b/docs/namespaces.html index ea4cdfd..063713e 100644 --- a/docs/namespaces.html +++ b/docs/namespaces.html @@ -87,21 +87,28 @@  Nchoose_filter_thresholdsDefine QC filter thresholds using a MAD-based approach  COptionsOptions for compute()  CResultsResults of compute() - Nfind_median_madCalculate the median and MAD from an array of values - COptionsOptions for find_median_mad::compute() - CResultsContainer for the median and MAD - CWorkspaceTemporary data structures for compute_blocked() - Nper_cell_qc_metricsCompute per-cell quality control metrics - CBuffersBuffers for direct storage of the calculated statistics - COptionsOptions for compute() - CResultsResult store for QC metric calculations - Nrna_quality_controlSimple per-cell QC metrics from an RNA count matrix - CBlockedFiltersFilter for high-quality cells using RNA-based metrics with blocking - CFiltersFilter for high-quality cells using RNA-based metrics - CFiltersOptionsOptions for Filters() - CMetricsBuffersBuffers for direct storage of the calculated statistics - CMetricsOptionsOptions for compute_metrics() - CMetricsResultsResults of the QC metric calculations + Ncrispr_quality_controlSimple per-cell QC metrics from a CRISPR count matrix + CBlockedFiltersFilter for high-quality cells using CRISPR-based metrics with blocking + CFiltersFilter for high-quality cells using CRISPR-based metrics + CFiltersOptionsOptions for Filters() + CMetricsBuffersBuffers for direct storage of the calculated statistics + CMetricsOptionsOptions for compute_metrics() + CMetricsResultsResults of the QC metric calculations + Nfind_median_madCalculate the median and MAD from an array of values + COptionsOptions for find_median_mad::compute() + CResultsContainer for the median and MAD + CWorkspaceTemporary data structures for compute_blocked() + Nper_cell_qc_metricsCompute per-cell quality control metrics + CBuffersBuffers for direct storage of the calculated statistics + COptionsOptions for compute() + CResultsResult store for QC metric calculations + Nrna_quality_controlSimple per-cell QC metrics from an RNA count matrix + CBlockedFiltersFilter for high-quality cells using RNA-based metrics with blocking + CFiltersFilter for high-quality cells using RNA-based metrics + CFiltersOptionsOptions for Filters() + CMetricsBuffersBuffers for direct storage of the calculated statistics + CMetricsOptionsOptions for compute_metrics() + CMetricsResultsResults of the QC metric calculations diff --git a/docs/namespacescran.html b/docs/namespacescran.html index 1c76465..bb22659 100644 --- a/docs/namespacescran.html +++ b/docs/namespacescran.html @@ -88,6 +88,9 @@ namespace  choose_filter_thresholds  Define QC filter thresholds using a MAD-based approach.
                    +namespace  crispr_quality_control + Simple per-cell QC metrics from a CRISPR count matrix.
                  +  namespace  find_median_mad  Calculate the median and MAD from an array of values.
                    diff --git a/docs/namespacescran_1_1crispr__quality__control.html b/docs/namespacescran_1_1crispr__quality__control.html new file mode 100644 index 0000000..1b192be --- /dev/null +++ b/docs/namespacescran_1_1crispr__quality__control.html @@ -0,0 +1,477 @@ + + + + + + + +scran_quality_control: scran::crispr_quality_control Namespace Reference + + + + + + + + + + +
                  +
                  + + + + + + +
                  +
                  scran_quality_control +
                  +
                  Compute simple per-cell quality control metrics
                  +
                  +
                  + + + + + + + + +
                  +
                  + + +
                  +
                  +
                  +
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                  scran::crispr_quality_control Namespace Reference
                  +
                  +
                  + +

                  Simple per-cell QC metrics from a CRISPR count matrix. +More...

                  + + + + + + + + + + + + + + + + + + + + +

                  +Classes

                  class  BlockedFilters
                   Filter for high-quality cells using CRISPR-based metrics with blocking. More...
                   
                  class  Filters
                   Filter for high-quality cells using CRISPR-based metrics. More...
                   
                  struct  FiltersOptions
                   Options for Filters(). More...
                   
                  struct  MetricsBuffers
                   Buffers for direct storage of the calculated statistics. More...
                   
                  struct  MetricsOptions
                   Options for compute_metrics(). More...
                   
                  struct  MetricsResults
                   Results of the QC metric calculations. More...
                   
                  + + + + + + + + + + + + + + + + + + + +

                  +Functions

                  template<typename Value_ , typename Index_ , typename Sum_ , typename Detected_ >
                  void compute_metrics (const tatami::Matrix< Value_, Index_ > *mat, MetricsBuffers< Sum_, Detected_, Value_, Index_ > &output, const MetricsOptions &options)
                   
                  template<typename Sum_ = double, typename Detected_ = int, typename Value_ = double, typename Index_ = int>
                  MetricsResults< Sum_, Detected_, Value_, Index_ > compute_metrics (const tatami::Matrix< Value_, Index_ > *mat, const MetricsOptions &options)
                   
                  template<typename Float_ = double, typename Sum_ = double, typename Detected_ = int, typename Value_ = double, typename Index_ = int>
                  Filters< Float_ > compute_filters (size_t num, const MetricsBuffers< Sum_, Detected_, Value_, Index_ > &metrics, const FiltersOptions &options)
                   
                  template<typename Float_ = double, typename Sum_ = double, typename Detected_ = int, typename Value_ = double, typename Index_ = int>
                  Filters< Float_ > compute_filters (const MetricsResults< Sum_, Detected_, Value_, Index_ > &metrics, const FiltersOptions &options)
                   
                  template<typename Float_ = double, typename Sum_ = double, typename Detected_ = int, typename Value_ = double, typename Index_ = int, typename Block_ = int>
                  BlockedFilters< Float_ > compute_filters_blocked (size_t num, const MetricsBuffers< Sum_, Detected_, Value_, Index_ > &metrics, const Block_ *block, const FiltersOptions &options)
                   
                  template<typename Float_ = double, typename Sum_ = double, typename Detected_ = int, typename Value_ = double, typename Index_ = int, typename Block_ = int>
                  BlockedFilters< Float_ > compute_filters_blocked (const MetricsResults< Sum_, Detected_, Value_, Index_ > &metrics, const Block_ *block, const FiltersOptions &options)
                   
                  +

                  Detailed Description

                  +

                  Simple per-cell QC metrics from a CRISPR count matrix.

                  +

                  Given a feature-by-cell guide count matrix, this class computes several QC metrics:

                  +
                    +
                  • The sum of counts for each cell. Low counts indicate that the cell was not successfully transfected with a construct, or that library preparation and sequencing failed.
                  • +
                  • The number of detected guides per cell. In theory, this should be 1, as each cell should express no more than one guide construct. However, ambient contamination may introduce non-zero counts for multiple guides, without necessarily interfering with downstream analyses. As such, this metric is less useful for guide data, though we compute it anyway.
                  • +
                  • The maximum count in the most abundant guide construct. Low values indicate that the cell was not successfully transfected, or that library preparation and sequencing failed. The identity of the most abundant guide is also reported.
                  • +
                  +

                  Low-quality cells are defined as those with a low maximum count. Directly defining a threshold on the maximum count is somewhat tricky as unsuccessful transfection is not uncommon. This often results in a large subpopulation with low maximum counts, inflating the MAD and compromising the threshold calculation. Instead, we use the following approach:

                  +
                    +
                  1. Compute the median of the proportion of counts in the most abundant guide (i.e., the maximum proportion),
                  2. +
                  3. Subset the cells to only those with maximum proportions above the median,
                  4. +
                  5. Define a threshold for low outliers on the log-transformed maximum count within the subset.
                  6. +
                  +

                  This assumes that over 50% of cells were successfully transfected with a single guide construct and have high maximum proportions. In contrast, unsuccessful transfections will be dominated by ambient contamination and have low proportions. By taking the subset above the median proportion, we remove all of the unsuccessful transfections and enrich for mostly-high-quality cells. From there, we can apply the usual outlier detection methods on the maximum count, with log-transformation to avoid a negative threshold.

                  +

                  Keep in mind that the maximum proportion is only used to define the subset for threshold calculation. Once the maximum count threshold is computed, they are applied to all cells, regardless of their maximum proportions. This allows us to recover good cells that would have been filtered out by our aggressive median subset. It also ensures that we do not remove cells transfected with multiple guides - such cells are not necessarily uninteresting, e.g., for examining interaction effects, so we will err on the side of caution and leave them in.

                  +

                  Function Documentation

                  + +

                  ◆ compute_metrics() [1/2]

                  + +
                  +
                  +
                  +template<typename Value_ , typename Index_ , typename Sum_ , typename Detected_ >
                  + + + + + + + + + + + + + + + + + + + + + + + + +
                  void scran::crispr_quality_control::compute_metrics (const tatami::Matrix< Value_, Index_ > * mat,
                  MetricsBuffers< Sum_, Detected_, Value_, Index_ > & output,
                  const MetricsOptionsoptions 
                  )
                  +
                  +

                  Compute the QC metrics from an input matrix. This is a wrapper around per_cell_qc_metrics::compute() with some pre-configuration for CRISPR-relevant metrics.

                  +
                  Template Parameters
                  + + + + + +
                  Value_Type of matrix value.
                  Index_Type of the matrix indices.
                  Sum_Numeric type to store the summed expression.
                  Detected_Integer type to store the number of cells.
                  +
                  +
                  +
                  Parameters
                  + + + + +
                  matPointer to a feature-by-cells matrix containing counts.
                  [out]outputMetricsBuffers object in which to store the output.
                  optionsFurther options.
                  +
                  +
                  + +
                  +
                  + +

                  ◆ compute_metrics() [2/2]

                  + +
                  +
                  +
                  +template<typename Sum_ = double, typename Detected_ = int, typename Value_ = double, typename Index_ = int>
                  + + + + + + + + + + + + + + + + + + +
                  MetricsResults< Sum_, Detected_, Value_, Index_ > scran::crispr_quality_control::compute_metrics (const tatami::Matrix< Value_, Index_ > * mat,
                  const MetricsOptionsoptions 
                  )
                  +
                  +

                  Overload of compute_metrics() that allocates memory for the results.

                  +
                  Template Parameters
                  + + + + + + +
                  Sum_Numeric type to store the summed expression.
                  Detected_Integer type to store the number of cells.
                  Value_Type of matrix value.
                  Index_Type of the matrix indices.
                  Subset_Either a pointer to an array of booleans or a vector of indices.
                  +
                  +
                  +
                  Parameters
                  + + + + +
                  matPointer to a feature-by-cells tatami matrix containing counts.
                  [in]subsetsVector of feature subsets, see per_cell_qc_metrics::compute() for details.
                  optionsFurther options.
                  +
                  +
                  +
                  Returns
                  A PerCellRnaQcMetrics::Results object containing the QC metrics. Subset proportions are returned depending on the subsets.
                  + +
                  +
                  + +

                  ◆ compute_filters() [1/2]

                  + +
                  +
                  +
                  +template<typename Float_ = double, typename Sum_ = double, typename Detected_ = int, typename Value_ = double, typename Index_ = int>
                  + + + + + + + + + + + + + + + + + + + + + + + + +
                  Filters< Float_ > scran::crispr_quality_control::compute_filters (size_t num,
                  const MetricsBuffers< Sum_, Detected_, Value_, Index_ > & metrics,
                  const FiltersOptionsoptions 
                  )
                  +
                  +
                  Template Parameters
                  + + + + + + +
                  Float_Floating-point type for the thresholds.
                  Sum_Numeric type to store the summed expression.
                  Detected_Integer type to store the number of cells.
                  Value_Type of matrix value.
                  Index_Type of the matrix indices.
                  +
                  +
                  +
                  Parameters
                  + + + + + +
                  numNumber of cells.
                  metricsA collection of arrays containing CRISPR-based QC metrics, filled by compute_metrics(). MetricsBuffers::subset_sum is assumed to contain the sums of negative control feature subsets like IgG antibodies.
                  optionsFurther options for filtering.
                  Filtersto be applied to CRISPR-based QC metrics.
                  +
                  +
                  + +
                  +
                  + +

                  ◆ compute_filters() [2/2]

                  + +
                  +
                  +
                  +template<typename Float_ = double, typename Sum_ = double, typename Detected_ = int, typename Value_ = double, typename Index_ = int>
                  + + + + + + + + + + + + + + + + + + +
                  Filters< Float_ > scran::crispr_quality_control::compute_filters (const MetricsResults< Sum_, Detected_, Value_, Index_ > & metrics,
                  const FiltersOptionsoptions 
                  )
                  +
                  +
                  Template Parameters
                  + + + + + + +
                  Float_Floating-point type for the thresholds.
                  Sum_Numeric type to store the summed expression.
                  Detected_Integer type to store the number of cells.
                  Value_Type of matrix value.
                  Index_Type of the matrix indices.
                  +
                  +
                  +
                  Parameters
                  + + + + +
                  metricsCRISPR-based QC metrics from compute_metrics(). MetricsBuffers::subset_sum is assumed to contain the sums of negative control feature subsets like IgG antibodies.
                  optionsFurther options for filtering.
                  Filtersto be applied to CRISPR-based QC metrics.
                  +
                  +
                  + +
                  +
                  + +

                  ◆ compute_filters_blocked() [1/2]

                  + +
                  +
                  +
                  +template<typename Float_ = double, typename Sum_ = double, typename Detected_ = int, typename Value_ = double, typename Index_ = int, typename Block_ = int>
                  + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
                  BlockedFilters< Float_ > scran::crispr_quality_control::compute_filters_blocked (size_t num,
                  const MetricsBuffers< Sum_, Detected_, Value_, Index_ > & metrics,
                  const Block_ * block,
                  const FiltersOptionsoptions 
                  )
                  +
                  +
                  Template Parameters
                  + + + + + + +
                  Sum_Numeric type to store the summed expression.
                  Detected_Integer type to store the number of cells.
                  Value_Type of matrix value.
                  Index_Type of the matrix indices.
                  Block_Integer type for the block assignments.
                  +
                  +
                  +
                  Parameters
                  + + + + + +
                  numNumber of cells.
                  metricsA collection of arrays containing CRISPR-based QC metrics, filled by compute_metrics().
                  [in]blockPointer to an array of length num containing block identifiers. Values should be integer IDs in $[0, N)$ where $N$ is the number of blocks.
                  optionsFurther options for filtering.
                  +
                  +
                  +
                  Returns
                  Filters to be applied to blocks of CRISPR-based QC metrics.
                  + +
                  +
                  + +

                  ◆ compute_filters_blocked() [2/2]

                  + +
                  +
                  +
                  +template<typename Float_ = double, typename Sum_ = double, typename Detected_ = int, typename Value_ = double, typename Index_ = int, typename Block_ = int>
                  + + + + + + + + + + + + + + + + + + + + + + + + +
                  BlockedFilters< Float_ > scran::crispr_quality_control::compute_filters_blocked (const MetricsResults< Sum_, Detected_, Value_, Index_ > & metrics,
                  const Block_ * block,
                  const FiltersOptionsoptions 
                  )
                  +
                  +
                  Template Parameters
                  + + + + + + +
                  Sum_Numeric type to store the summed expression.
                  Detected_Integer type to store the number of cells.
                  Value_Type of matrix value.
                  Index_Type of the matrix indices.
                  Block_Integer type for the block assignments.
                  +
                  +
                  +
                  Parameters
                  + + + + +
                  metricsCRISPR-based QC metrics computed by compute_metrics().
                  [in]blockPointer to an array of length num containing block identifiers. Values should be integer IDs in $[0, N)$ where $N$ is the number of blocks.
                  optionsFurther options for filtering.
                  +
                  +
                  +
                  Returns
                  Filters to be applied to blocks of CRISPR-based QC metrics.
                  + +
                  +
                  +
                  + + + + diff --git a/docs/per__cell__qc__metrics_8hpp.html b/docs/per__cell__qc__metrics_8hpp.html index fc7c0ac..b14c3e3 100644 --- a/docs/per__cell__qc__metrics_8hpp.html +++ b/docs/per__cell__qc__metrics_8hpp.html @@ -116,11 +116,13 @@
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scran::crispr_quality_control::MetricsBuffers + scran::crispr_quality_control::MetricsResults + scran::crispr_quality_control::FiltersOptions + scran::crispr_quality_control::Filters + scran::crispr_quality_control::BlockedFilters + scran + scran::crispr_quality_control + find_median_mad.hpp scran/ @@ -129,6 +145,53 @@ (const MetricsResults< Sum_, Detected_ > &metrics, const Block_ *block) const + + scran::crispr_quality_control::BlockedFilters + classscran_1_1crispr__quality__control_1_1BlockedFilters.html + typename Float_ + + + BlockedFilters + classscran_1_1crispr__quality__control_1_1BlockedFilters.html + a402004aa5474729739a234c4e53aac95 + ()=default + + + const std::vector< Float_ > & + get_max_value + classscran_1_1crispr__quality__control_1_1BlockedFilters.html + a738a223db413ed6cf69ef8d7899a0935 + () const + + + std::vector< Float_ > & + get_max_value + classscran_1_1crispr__quality__control_1_1BlockedFilters.html + a0ebca01693da9084577412ae3e32216a + () + + + void + filter + classscran_1_1crispr__quality__control_1_1BlockedFilters.html + af98d5546e74c7500c373a97626411514 + (size_t num, const MetricsBuffers< Sum_, Detected_, Value_, Index_ > &metrics, const Block_ *block, Output_ *output) const + + + void + filter + classscran_1_1crispr__quality__control_1_1BlockedFilters.html + acf4ed3bf581e289236521bf7ddd084b1 + (const MetricsResults< Sum_, Detected_, Value_, Index_ > &metrics, const Block_ *block, Output_ *output) const + + + std::vector< Output_ > + filter + classscran_1_1crispr__quality__control_1_1BlockedFilters.html + aa05dbd507a7b01d75c221336d123826e + (const MetricsResults< Sum_, Detected_, Value_, Index_ > &metrics, const Block_ *block) const + + scran::rna_quality_control::BlockedFilters classscran_1_1rna__quality__control_1_1BlockedFilters.html @@ -315,6 +378,53 @@ (const MetricsResults< Sum_, Detected_ > &metrics) const + + scran::crispr_quality_control::Filters + classscran_1_1crispr__quality__control_1_1Filters.html + typename Float_ + + + Filters + classscran_1_1crispr__quality__control_1_1Filters.html + ae67b5c6cf4bd2c066937be1873f174e8 + ()=default + + + Float_ + get_max_value + classscran_1_1crispr__quality__control_1_1Filters.html + a05128c13ad180f0da43444ce14203ffe + () const + + + Float_ & + get_max_value + classscran_1_1crispr__quality__control_1_1Filters.html + accd99968f2487317178c7f52dd5fede2 + () + + + void + filter + classscran_1_1crispr__quality__control_1_1Filters.html + af819567873395d1befb493a542ca586e + (size_t num, const MetricsBuffers< Sum_, Detected_, Value_, Index_ > &metrics, Output_ *output) const + + + void + filter + classscran_1_1crispr__quality__control_1_1Filters.html + a2831a85ee73edd21326c7c9d7fd81de7 + (const MetricsResults< Sum_, Detected_, Value_, Index_ > &metrics, Output_ *output) const + + + std::vector< Output_ > + filter + classscran_1_1crispr__quality__control_1_1Filters.html + aed0aff71c39a3f783b8a8c553fb930d1 + (const MetricsResults< Sum_, Detected_, Value_, Index_ > &metrics) const + + scran::rna_quality_control::Filters classscran_1_1rna__quality__control_1_1Filters.html @@ -415,6 +525,17 @@ + + scran::crispr_quality_control::FiltersOptions + structscran_1_1crispr__quality__control_1_1FiltersOptions.html + + double + max_value_num_mads + structscran_1_1crispr__quality__control_1_1FiltersOptions.html + a190ecbb3c51fe7d9b389f93eb64bca94 + + + scran::rna_quality_control::FiltersOptions structscran_1_1rna__quality__control_1_1FiltersOptions.html @@ -467,6 +588,42 @@ + + scran::crispr_quality_control::MetricsBuffers + structscran_1_1crispr__quality__control_1_1MetricsBuffers.html + typename Sum_ + typename Detected_ + typename Value_ + typename Index_ + + Sum_ * + sum + structscran_1_1crispr__quality__control_1_1MetricsBuffers.html + abc73760fe659f64ad87b5ec73c37f587 + + + + Detected_ * + detected + structscran_1_1crispr__quality__control_1_1MetricsBuffers.html + adc50f314b70791110d0160ff650433e2 + + + + Value_ * + max_value + structscran_1_1crispr__quality__control_1_1MetricsBuffers.html + ad0e2d7df3f528fa07759d232b226e9bc + + + + Index_ * + max_index + structscran_1_1crispr__quality__control_1_1MetricsBuffers.html + a88f7021de51b618ebaf26b3c6725213a + + + scran::rna_quality_control::MetricsBuffers structscran_1_1rna__quality__control_1_1MetricsBuffers.html @@ -506,6 +663,17 @@ + + scran::crispr_quality_control::MetricsOptions + structscran_1_1crispr__quality__control_1_1MetricsOptions.html + + int + num_threads + structscran_1_1crispr__quality__control_1_1MetricsOptions.html + a64fcc3fc16105fe2c18b6cb1b54b5e09 + + + scran::rna_quality_control::MetricsOptions structscran_1_1rna__quality__control_1_1MetricsOptions.html @@ -544,6 +712,42 @@ + + scran::crispr_quality_control::MetricsResults + structscran_1_1crispr__quality__control_1_1MetricsResults.html + typename Sum_ + typename Detected_ + typename Value_ + typename Index_ + + std::vector< Sum_ > + sum + structscran_1_1crispr__quality__control_1_1MetricsResults.html + ae690960c50586e767de0a36f65dac802 + + + + std::vector< Detected_ > + detected + structscran_1_1crispr__quality__control_1_1MetricsResults.html + a5e8a29d574034718c109c49185dcea85 + + + + std::vector< Value_ > + max_value + structscran_1_1crispr__quality__control_1_1MetricsResults.html + adbd58b52aef9b893b72499323c07fdfc + + + + std::vector< Index_ > + max_index + structscran_1_1crispr__quality__control_1_1MetricsResults.html + a0779ecebf71e3fe6df1a927ad3017af1 + + + scran::rna_quality_control::MetricsResults structscran_1_1rna__quality__control_1_1MetricsResults.html @@ -802,6 +1006,7 @@ namespacescran.html scran::adt_quality_control scran::choose_filter_thresholds + scran::crispr_quality_control scran::find_median_mad scran::per_cell_qc_metrics scran::rna_quality_control @@ -899,6 +1104,58 @@ (Index_ num, const Value_ *metrics, const Block_ *block, find_median_mad::Workspace< Float_, Index_ > *workspace, const Options &options) + + scran::crispr_quality_control + namespacescran_1_1crispr__quality__control.html + scran::crispr_quality_control::BlockedFilters + scran::crispr_quality_control::Filters + scran::crispr_quality_control::FiltersOptions + scran::crispr_quality_control::MetricsBuffers + scran::crispr_quality_control::MetricsOptions + scran::crispr_quality_control::MetricsResults + + void + compute_metrics + namespacescran_1_1crispr__quality__control.html + a5e0a41f185fd86479db5ef8a7e5d4116 + (const tatami::Matrix< Value_, Index_ > *mat, MetricsBuffers< Sum_, Detected_, Value_, Index_ > &output, const MetricsOptions &options) + + + MetricsResults< Sum_, Detected_, Value_, Index_ > + compute_metrics + namespacescran_1_1crispr__quality__control.html + a5456326ad2cfe939762f0f79d2e9489b + (const tatami::Matrix< Value_, Index_ > *mat, const MetricsOptions &options) + + + Filters< Float_ > + compute_filters + namespacescran_1_1crispr__quality__control.html + a376b9b86602e1beef8b58270ec616063 + (size_t num, const MetricsBuffers< Sum_, Detected_, Value_, Index_ > &metrics, const FiltersOptions &options) + + + Filters< Float_ > + compute_filters + namespacescran_1_1crispr__quality__control.html + abc592b0d390ca248c7796ff4333d7aff + (const MetricsResults< Sum_, Detected_, Value_, Index_ > &metrics, const FiltersOptions &options) + + + BlockedFilters< Float_ > + compute_filters_blocked + namespacescran_1_1crispr__quality__control.html + a3c7e3955d25ac8111974ea44fea05ed9 + (size_t num, const MetricsBuffers< Sum_, Detected_, Value_, Index_ > &metrics, const Block_ *block, const FiltersOptions &options) + + + BlockedFilters< Float_ > + compute_filters_blocked + namespacescran_1_1crispr__quality__control.html + a41e3134f0f14330ec702ce2421e5a96b + (const MetricsResults< Sum_, Detected_, Value_, Index_ > &metrics, const Block_ *block, const FiltersOptions &options) + + scran::find_median_mad namespacescran_1_1find__median__mad.html diff --git a/docs/search/all_1.js 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                  scran_quality_control +
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                  Compute simple per-cell quality control metrics
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                  scran::crispr_quality_control::FiltersOptions Member List
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                  + + + + diff --git a/docs/structscran_1_1crispr__quality__control_1_1FiltersOptions.html b/docs/structscran_1_1crispr__quality__control_1_1FiltersOptions.html new file mode 100644 index 0000000..04c5393 --- /dev/null +++ b/docs/structscran_1_1crispr__quality__control_1_1FiltersOptions.html @@ -0,0 +1,122 @@ + + + + + + + +scran_quality_control: scran::crispr_quality_control::FiltersOptions Struct Reference + + + + + + + + + + +
                  +
                  + + + + + + +
                  +
                  scran_quality_control +
                  +
                  Compute simple per-cell quality control metrics
                  +
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                  scran::crispr_quality_control::FiltersOptions Struct Reference
                  +
                  +
                  + +

                  Options for Filters(). + More...

                  + +

                  #include <crispr_quality_control.hpp>

                  + + + + +

                  +Public Attributes

                  double max_value_num_mads = 3
                   
                  +

                  Detailed Description

                  +

                  Options for Filters().

                  +

                  Member Data Documentation

                  + +

                  ◆ max_value_num_mads

                  + +
                  +
                  + + + + +
                  double scran::crispr_quality_control::FiltersOptions::max_value_num_mads = 3
                  +
                  +

                  Number of MADs below the median, to define the threshold for outliers in the maximum count. This should be non-negative.

                  + +
                  +
                  +
                  The documentation for this struct was generated from the following file: +
                  + + + + diff --git a/docs/structscran_1_1crispr__quality__control_1_1MetricsBuffers-members.html b/docs/structscran_1_1crispr__quality__control_1_1MetricsBuffers-members.html new file mode 100644 index 0000000..df4be45 --- /dev/null +++ b/docs/structscran_1_1crispr__quality__control_1_1MetricsBuffers-members.html @@ -0,0 +1,94 @@ + + + + + + + +scran_quality_control: Member List + + + + + + + + + + +
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                  scran_quality_control +
                  +
                  Compute simple per-cell quality control metrics
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                  scran::crispr_quality_control::MetricsBuffers< Sum_, Detected_, Value_, Index_ > Member List
                  +
                  + + + + + diff --git a/docs/structscran_1_1crispr__quality__control_1_1MetricsBuffers.html b/docs/structscran_1_1crispr__quality__control_1_1MetricsBuffers.html new file mode 100644 index 0000000..996d0ce --- /dev/null +++ b/docs/structscran_1_1crispr__quality__control_1_1MetricsBuffers.html @@ -0,0 +1,191 @@ + + + + + + + +scran_quality_control: scran::crispr_quality_control::MetricsBuffers< Sum_, Detected_, Value_, Index_ > Struct Template Reference + + + + + + + + + + +
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                  scran_quality_control +
                  +
                  Compute simple per-cell quality control metrics
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                  scran::crispr_quality_control::MetricsBuffers< Sum_, Detected_, Value_, Index_ > Struct Template Reference
                  +
                  +
                  + +

                  Buffers for direct storage of the calculated statistics. + More...

                  + +

                  #include <crispr_quality_control.hpp>

                  + + + + + + + + + + +

                  +Public Attributes

                  Sum_ * sum = NULL
                   
                  Detected_ * detected = NULL
                   
                  Value_ * max_value = NULL
                   
                  Index_ * max_index = NULL
                   
                  +

                  Detailed Description

                  +
                  template<typename Sum_ = double, typename Detected_ = int, typename Value_ = double, typename Index_ = int>
                  +struct scran::crispr_quality_control::MetricsBuffers< Sum_, Detected_, Value_, Index_ >

                  Buffers for direct storage of the calculated statistics.

                  +
                  Template Parameters
                  + + + + + +
                  Sum_Numeric type to store the summed expression.
                  Detected_Integer type to store the number of cells.
                  Value_Type of matrix value.
                  Index_Type of the matrix indices.
                  +
                  +
                  +

                  Member Data Documentation

                  + +

                  ◆ sum

                  + +
                  +
                  +
                  +template<typename Sum_ = double, typename Detected_ = int, typename Value_ = double, typename Index_ = int>
                  + + + + +
                  Sum_* scran::crispr_quality_control::MetricsBuffers< Sum_, Detected_, Value_, Index_ >::sum = NULL
                  +
                  +

                  Pointer to an array of length equal to the number of cells, see MetricsResults::sum. This should not be NULL when calling compute_metrics().

                  + +
                  +
                  + +

                  ◆ detected

                  + +
                  +
                  +
                  +template<typename Sum_ = double, typename Detected_ = int, typename Value_ = double, typename Index_ = int>
                  + + + + +
                  Detected_* scran::crispr_quality_control::MetricsBuffers< Sum_, Detected_, Value_, Index_ >::detected = NULL
                  +
                  +

                  Pointer to an array of length equal to the number of cells, see MetricsResults::detected. This should not be NULL when calling compute_metrics().

                  + +
                  +
                  + +

                  ◆ max_value

                  + +
                  +
                  +
                  +template<typename Sum_ = double, typename Detected_ = int, typename Value_ = double, typename Index_ = int>
                  + + + + +
                  Value_* scran::crispr_quality_control::MetricsBuffers< Sum_, Detected_, Value_, Index_ >::max_value = NULL
                  +
                  +

                  Pointer to an array of length equal to the number of cells, see MetricsResults::max_value. This should not be NULL when calling compute_metrics().

                  + +
                  +
                  + +

                  ◆ max_index

                  + +
                  +
                  +
                  +template<typename Sum_ = double, typename Detected_ = int, typename Value_ = double, typename Index_ = int>
                  + + + + +
                  Index_* scran::crispr_quality_control::MetricsBuffers< Sum_, Detected_, Value_, Index_ >::max_index = NULL
                  +
                  +

                  Pointer to an array of length equal to the number of cells, see MetricsResults::max_index. This should not be NULL when calling compute_metrics().

                  + +
                  +
                  +
                  The documentation for this struct was generated from the following file: +
                  + + + + diff --git a/docs/structscran_1_1crispr__quality__control_1_1MetricsOptions-members.html b/docs/structscran_1_1crispr__quality__control_1_1MetricsOptions-members.html new file mode 100644 index 0000000..e450a74 --- /dev/null +++ b/docs/structscran_1_1crispr__quality__control_1_1MetricsOptions-members.html @@ -0,0 +1,91 @@ + + + + + + + +scran_quality_control: Member List + + + + + + + + + + +
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                  +
                  scran_quality_control +
                  +
                  Compute simple per-cell quality control metrics
                  +
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                  scran::crispr_quality_control::MetricsOptions Member List
                  +
                  +
                  + +

                  This is the complete list of members for scran::crispr_quality_control::MetricsOptions, including all inherited members.

                  + + +
                  num_threadsscran::crispr_quality_control::MetricsOptions
                  + + + + diff --git a/docs/structscran_1_1crispr__quality__control_1_1MetricsOptions.html b/docs/structscran_1_1crispr__quality__control_1_1MetricsOptions.html new file mode 100644 index 0000000..491b5b2 --- /dev/null +++ b/docs/structscran_1_1crispr__quality__control_1_1MetricsOptions.html @@ -0,0 +1,122 @@ + + + + + + + +scran_quality_control: scran::crispr_quality_control::MetricsOptions Struct Reference + + + + + + + + + + +
                  +
                  + + + + + + +
                  +
                  scran_quality_control +
                  +
                  Compute simple per-cell quality control metrics
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                  scran::crispr_quality_control::MetricsOptions Struct Reference
                  +
                  +
                  + +

                  Options for compute_metrics(). + More...

                  + +

                  #include <crispr_quality_control.hpp>

                  + + + + +

                  +Public Attributes

                  int num_threads = 1
                   
                  +

                  Detailed Description

                  +

                  Options for compute_metrics().

                  +

                  Member Data Documentation

                  + +

                  ◆ num_threads

                  + +
                  +
                  + + + + +
                  int scran::crispr_quality_control::MetricsOptions::num_threads = 1
                  +
                  +

                  Number of threads to use.

                  + +
                  +
                  +
                  The documentation for this struct was generated from the following file: +
                  + + + + diff --git a/docs/structscran_1_1crispr__quality__control_1_1MetricsResults-members.html b/docs/structscran_1_1crispr__quality__control_1_1MetricsResults-members.html new file mode 100644 index 0000000..1f7829e --- /dev/null +++ b/docs/structscran_1_1crispr__quality__control_1_1MetricsResults-members.html @@ -0,0 +1,94 @@ + + + + + + + +scran_quality_control: Member List + + + + + + + + + + +
                  +
                  + + + + + + +
                  +
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                  +
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                  scran::crispr_quality_control::MetricsResults< Sum_, Detected_, Value_, Index_ > Member List
                  +
                  + + + + + diff --git a/docs/structscran_1_1crispr__quality__control_1_1MetricsResults.html b/docs/structscran_1_1crispr__quality__control_1_1MetricsResults.html new file mode 100644 index 0000000..febf8f0 --- /dev/null +++ b/docs/structscran_1_1crispr__quality__control_1_1MetricsResults.html @@ -0,0 +1,192 @@ + + + + + + + +scran_quality_control: scran::crispr_quality_control::MetricsResults< Sum_, Detected_, Value_, Index_ > Struct Template Reference + + + + + + + + + + +
                  +
                  + + + + + + +
                  +
                  scran_quality_control +
                  +
                  Compute simple per-cell quality control metrics
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                  scran::crispr_quality_control::MetricsResults< Sum_, Detected_, Value_, Index_ > Struct Template Reference
                  +
                  +
                  + +

                  Results of the QC metric calculations. + More...

                  + +

                  #include <crispr_quality_control.hpp>

                  + + + + + + + + + + +

                  +Public Attributes

                  std::vector< Sum_ > sum
                   
                  std::vector< Detected_ > detected
                   
                  std::vector< Value_ > max_value
                   
                  std::vector< Index_ > max_index
                   
                  +

                  Detailed Description

                  +
                  template<typename Sum_ = double, typename Detected_ = int, typename Value_ = double, typename Index_ = int>
                  +struct scran::crispr_quality_control::MetricsResults< Sum_, Detected_, Value_, Index_ >

                  Results of the QC metric calculations.

                  +
                  Template Parameters
                  + + + + + +
                  Sum_Numeric type to store the summed expression.
                  Detected_Integer type to store the number of cells.
                  Value_Type of matrix value.
                  Index_Type of the matrix indices.
                  +
                  +
                  +

                  Meaningful instances of this object should generally be constructed by calling the compute_metrics() function.

                  +

                  Member Data Documentation

                  + +

                  ◆ sum

                  + +
                  +
                  +
                  +template<typename Sum_ = double, typename Detected_ = int, typename Value_ = double, typename Index_ = int>
                  + + + + +
                  std::vector<Sum_> scran::crispr_quality_control::MetricsResults< Sum_, Detected_, Value_, Index_ >::sum
                  +
                  +

                  Vector of length equal to the number of cells in the dataset, containing the sum of counts for each cell.

                  + +
                  +
                  + +

                  ◆ detected

                  + +
                  +
                  +
                  +template<typename Sum_ = double, typename Detected_ = int, typename Value_ = double, typename Index_ = int>
                  + + + + +
                  std::vector<Detected_> scran::crispr_quality_control::MetricsResults< Sum_, Detected_, Value_, Index_ >::detected
                  +
                  +

                  Vector of length equal to the number of cells in the dataset, containing the number of detected features in each cell.

                  + +
                  +
                  + +

                  ◆ max_value

                  + +
                  +
                  +
                  +template<typename Sum_ = double, typename Detected_ = int, typename Value_ = double, typename Index_ = int>
                  + + + + +
                  std::vector<Value_> scran::crispr_quality_control::MetricsResults< Sum_, Detected_, Value_, Index_ >::max_value
                  +
                  +

                  Vector of length equal to the number of cells in the dataset, containing the maximum count for each cell.

                  + +
                  +
                  + +

                  ◆ max_index

                  + +
                  +
                  +
                  +template<typename Sum_ = double, typename Detected_ = int, typename Value_ = double, typename Index_ = int>
                  + + + + +
                  std::vector<Index_> scran::crispr_quality_control::MetricsResults< Sum_, Detected_, Value_, Index_ >::max_index
                  +
                  +

                  Vector of length equal to the number of cells in the dataset, containing the row index of the guide with the maximum count for each cell.

                  + +
                  +
                  +
                  The documentation for this struct was generated from the following file: +
                  + + + +