fix man pages

.github/workflows/check-bioc.yml

@@ -19,7 +19,7 @@ jobs:
       fail-fast: false
       matrix:
         config:
-        # - { os: windows-latest, bioc: 'devel'}
+        - { os: windows-latest, bioc: 'devel'}
         - { os: macOS-latest, bioc: 'devel', curlConfigPath: '/usr/bin/'}
         - { os: ubuntu-latest, bioc: 'devel'}
 #        - { os: ubuntu-latest, bioc: 'devel', cran: "https://demo.rstudiopm.com/all/__linux__/xenial/latest"}

man/VcfBasicRules-class.Rd

@@ -157,12 +157,12 @@ In the following code snippets \code{x}, \code{values}, and \code{...}
 are objects from any of the classes described in this help page, or
 \code{VcfFilterRules}.
 
-\describe{
-    \item{}{
+\itemize{
+    \item{
     \code{append(x, values, after = length(x))}:
     Appends the values onto \code{x} at the index given by \code{after}.
     }
-    \item{}{
+    \item{
     \code{c(x, ...,)}:
     Concatenates the filters objects in \code{...} onto the end of \code{x}.
     }
@@ -175,8 +175,8 @@ produces a \code{VcfFilterRules} object.
 
 \section{Evaluating}{
 As described in the \code{S4Vectors} documentation:
-\describe{
-\item{}{
+\itemize{
+\item{
     \code{eval(expr, envir, enclos)}:
     Evaluates a rule instance (passed as the \code{expr} argument)
     in their respective context of a \code{VCF} object
@@ -190,7 +190,7 @@ As described in the \code{S4Vectors} documentation:
     \item{\strong{\code{FilterRules}}: \code{envir}}
     }
 }
-\item{}{
+\item{
     \code{evalSeparately(expr, envir, enclos)}:
 
         \code{subsetByFilter(x, filter)}

man/VcfFilterRules-class.Rd

@@ -70,38 +70,36 @@ In the following code snippets \code{x} is a \code{VcfFilterRules} object.
 }
 
 \section{Constructors}{
-\describe{}{
 \code{VcfFilterRules(...)}
 constructs an \code{VcfFilterRules} object from
 \code{VcfFixedRules}, \code{VcfInfoRules}, \code{VcfVepRules},
 and \code{VcfFilterRules} objects in \code{...}.
 }
-}
 
 \section{Subsetting and Replacement}{
 In the code snippets below, \code{x} is a \code{VcfFilterRules} object.
 
-\describe{
-    \item{}{
+\itemize{
+    \item{
     \code{x[i, drop = TRUE]}: Subsets the filter rules using the
     same interface as for \code{\linkS4class{Vector}}.
     If all filter rules are of the same type and \code{drop=TRUE} (default),
     the resulting object is re-typed to the most specialised class,
     if possible. In other words, if all remaining filter rules are of
     type \code{"vep"}, the object will be type as \code{VcfVepRules}.
     }
-    \item{}{
+    \item{
     \code{x[[i]]}: Extracts an expression or function via the same interface
     as for \code{\linkS4class{List}}.
     }
-    \item{}{
+    \item{
     \code{x[i] <- value}: Replaces a filter rule by one of any valid class
     (\code{VcfFixedRules}, \code{VcfInfoRules}, \code{VcfVepRules}, or
     \code{VcfFilterRules}).
     The active state(s), name(s), and type(s) (if applicable)
     are transferred from \code{value}.
     }
-    \item{}{
+    \item{
     \code{x[[i]] <- value}: The same interface as for
     \code{\linkS4class{List}}. The default active state for new
     rules is \code{TRUE}.
@@ -116,12 +114,12 @@ while \code{values} and \code{...} are objects from any of the
 classes \code{VcfFixedRules}, \code{VcfInfoRules}, \code{VcfVepRules},
 or \code{VcfFilterRules}:
 
-\describe{
-    \item{}{
+\itemize{
+    \item{
     \code{append(x, values, after = length(x))}:
     Appends the values onto \code{x} at the index given by \code{after}.
     }
-    \item{}{
+    \item{
     \code{c(x, ...,)}:
     Concatenates the filters objects in \code{...} onto the end of \code{x}.
     }

man/parseCSQToGRanges.Rd

@@ -0,0 +1,95 @@
+\name{parseCSQToGRanges}
+
+\alias{parseCSQToGRanges}
+\alias{parseCSQToGRanges,VCF-method}
+
+\title{
+  Parse the CSQ column of a VCF object into a GRanges object
+}
+
+\description{
+  Parse the CSQ column in a VCF object returned from the Ensembl
+  Variant Effect Predictor (VEP).
+
+  \strong{**This method was rescued following the deprecation of the package
+  \code{ensemblVEP} in the Bioconductor release \code{3.20}.**}
+}
+
+\usage{
+\S4method{parseCSQToGRanges}{VCF}(x, VCFRowID=character(),
+    ..., info.key = "CSQ")
+}
+
+\arguments{
+  \item{x}{
+    A \code{VCF} object.
+  }
+  \item{VCFRowID}{
+    A \code{character} vector of rownames from the original VCF.
+    When provided, the result includes a metadata column named
+    \sQuote{VCFRowID} which maps the result back to the row
+    (variant) in the original VCF.
+
+    When \code{VCFRowID} is not provided no \sQuote{VCFRowID}
+    column is included.
+  }
+  \item{info.key}{
+    The name of the INFO key that VEP writes the consequences to in the output
+    (default is \code{CSQ}). This should only be used if something other that
+    \code{CSQ} was passed in the --vcf_info_field flag in the output options.
+  }
+  \item{\dots}{
+    Arguments passed to other methods. Currently not used.
+  }
+}
+
+\details{
+  \describe{
+    \item{-}{
+      When \code{ensemblVEP} returns a \code{VCF} object, the consequence data
+      are returned unparsed in the 'CSQ' INFO column. \code{parseCSQToGRanges}
+      parses these data into a \code{GRanges} object that is expanded to match
+      the dimension of the 'CSQ' data. Because each variant can have multiple
+      matches, the ranges in the \code{GRanges} are repeated.
+
+      If rownames from the original VCF are provided as \code{VCFRowID} a
+      metadata column is included in the result that maps back to the row
+      (variant) in the original VCF.  This option is only applicable when the
+      \code{info.key} field has data (is not empty).
+
+      If no \code{info.key} column is found the function returns the data in
+      \code{rowRanges()}.
+    }
+  }
+}
+
+\value{
+  Returns a \code{GRanges} object with consequence data as the
+  metadata columns. If no 'CSQ' column is found the \code{GRanges}
+  from \code{rowRanges()} is returned.
+}
+
+\author{
+  Valerie Obenchain, Kevin Rue-Albrecht
+}
+
+\references{
+  Ensembl VEP Home:
+  \url{http://uswest.ensembl.org/info/docs/tools/vep/index.html}
+}
+
+\examples{
+  library(VariantAnnotation)
+  file <- system.file("extdata", "moderate.vcf", package = "TVTB")
+  vep <- readVcf(file)
+
+  ## The returned 'CSQ' data are unparsed.
+  info(vep)$CSQ
+
+  ## Parse into a GRanges and include the 'VCFRowID' column.
+  vcf <- readVcf(file, "hg19")
+  csq <- parseCSQToGRanges(vep, VCFRowID=rownames(vcf))
+  csq[1:4]
+}
+
+\keyword{methods}

man/vepInPhenoLevel-methods.Rd

@@ -32,7 +32,7 @@ considered.
 }
     \item{vepCol}{
 VEP prediction fields; \code{character} vector of metadata columns in
-\code{ensemblVEP::parseCSQToGRanges(vcf)}.
+\code{parseCSQToGRanges(vcf)}.
 }
     \item{unique}{
 If \code{TRUE}, consider only variants unique to the phenotype level
@@ -66,7 +66,6 @@ Kevin Rue-Albrecht
 
 \seealso{
 \code{\linkS4class{VCF}},
-\code{\link{ensemblVEP}},
 \code{\linkS4class{GRanges}},
 and \code{\linkS4class{DataFrame}}.
 }

vignettes/VcfFilterRules.Rmd

@@ -168,7 +168,7 @@ fixedVcf <- colnames(fixed(vcf))
 fixedVcf
 infoVcf <- colnames(info(vcf))
 infoVcf
-csq <- ensemblVEP::parseCSQToGRanges(x = evcf)
+csq <- parseCSQToGRanges(x = evcf)
 vepVcf <- colnames(mcols(csq))
 vepVcf
 ```