README

This repository contains an R package, LDcompute to compute LD using SNPRelate functions and return results in a consistent format. It also includes an example wrapper script (compute_ld.R) and test data (testdata/) to show how it can be used.

Calling functions directly

Load other packages.

library(SeqArray)

Load the LDcompute package.

library(LDcompute)

## ℹ Loading LDcompute

Open the gds file:

gds <- seqOpen("testdata/1KG_phase3_subset.gds")

Choose the sample set:

sample_include <- seqGetData(gds, "sample.id")[1:500]

LD between a pair of variants

compute_ld_pair(gds, 1, 2, sample_include = sample_include)

## # A tibble: 1 x 3
##   variant.id.1 variant.id.2    ld_r2
##          <int>        <int>    <dbl>
## 1            1            2 0.000670

Using other methods:

compute_ld_pair(gds, 1, 2, sample_include = sample_include, ld_methods = c("r2", "dprime"))

## # A tibble: 1 x 4
##   variant.id.1 variant.id.2    ld_r2 ld_dprime
##          <int>        <int>    <dbl>     <dbl>
## 1            1            2 0.000670      1.00

LD between an index variant and a set of other variants

compute_ld_index(gds, 1, c(2:10), sample_include = sample_include)

## # A tibble: 9 x 3
##   variant.id.1 variant.id.2       ld_r2
##          <int>        <int>       <dbl>
## 1            1            2   0.000670 
## 2            1            3   0.0000162
## 3            1            4 NaN        
## 4            1            5   0.000198 
## 5            1            6   0.0000324
## 6            1            7 NaN        
## 7            1            8 NaN        
## 8            1            9   0.000181 
## 9            1           10   0.000463

Using other methods:

compute_ld_index(gds, 1, c(2:10), sample_include = sample_include, ld_methods = c("r2", "dprime"))

## # A tibble: 9 x 4
##   variant.id.1 variant.id.2       ld_r2 ld_dprime
##          <int>        <int>       <dbl>     <dbl>
## 1            1            2   0.000670       1.00
## 2            1            3   0.0000162      1.  
## 3            1            4 NaN            NaN   
## 4            1            5   0.000198       1.  
## 5            1            6   0.0000324      1.  
## 6            1            7 NaN            NaN   
## 7            1            8 NaN            NaN   
## 8            1            9   0.000181       1.  
## 9            1           10   0.000463       1.

LD between all pairs in a set of variants

compute_ld_set(gds, c(1:4), sample_include = sample_include)

## # A tibble: 6 x 3
##   variant.id.1 variant.id.2       ld_r2
##          <int>        <int>       <dbl>
## 1            1            2   0.000670 
## 2            1            3   0.0000162
## 3            1            4 NaN        
## 4            2            3   0.000166 
## 5            2            4 NaN        
## 6            3            4 NaN

Using other methods:

compute_ld_set(gds, c(1:4), sample_include = sample_include, ld_methods = c("r2", "dprime"))

## # A tibble: 6 x 4
##   variant.id.1 variant.id.2       ld_r2 ld_dprime
##          <int>        <int>       <dbl>     <dbl>
## 1            1            2   0.000670       1.00
## 2            1            3   0.0000162      1.  
## 3            1            4 NaN            NaN   
## 4            2            3   0.000166       1.00
## 5            2            4 NaN            NaN   
## 6            3            4 NaN            NaN

Cleanup

seqClose(gds)

Running compute_ld.R with test data

LD between a pair of variants

R --no-save --args \
  testdata/1KG_phase3_subset.gds \
  --ld_methods r2 dprime \
  --variant_include_file_1 testdata/variant_include_pair_1.rds \
  --variant_include_file_2 testdata/variant_include_pair_2.rds \
  --sample_include_file testdata/sample_include.rds \
  --out_prefix pair \
  < compute_ld.R

This creates a file called pair_ld.rds.

LD between an index variant and a set of other variants

R --no-save --args \
  testdata/1KG_phase3_subset.gds \
  --ld_methods r2 dprime \
  --variant_include_file_1 testdata/variant_include_index_1.rds \
  --variant_include_file_2 testdata/variant_include_index_2.rds \
  --sample_include_file testdata/sample_include.rds \
  --out_prefix index \
  < compute_ld.R

This creates a file called index_ld.rds.

LD between all pairs in a set of variants

R --no-save --args \
  testdata/1KG_phase3_subset.gds \
  --ld_methods r2 dprime \
  --variant_include_file_1 testdata/variant_include_set_1.rds \
  --sample_include_file testdata/sample_include.rds \
  --out_prefix set \
  < compute_ld.R

This creates a file called set_ld.rds.