54 lines
1.3 KiB
R
54 lines
1.3 KiB
R
\name{gsa.read.vcf}
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\alias{gsa.read.vcf}
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\title{
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gsa.read.vcf
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}
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\description{
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Reads a VCF file into a table. Optionally expands genotype columns into separate columns containing the genotype, separate from the other fields specified in the FORMAT field.
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}
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\usage{
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gsa.read.vcf(vcffile, skip=0, nrows=-1, expandGenotypeFields = FALSE)
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}
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\arguments{
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\item{vcffile}{
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The path to the vcf file.
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}
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\item{skip}{
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The number of lines of the data file to skip before beginning to read data.
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}
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\item{nrows}{
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The maximum number of rows to read in. Negative and other invalid values are ignored.
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}
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\item{expandGenotypeFields}{
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If TRUE, adds an additional column per sample containing just the genotype.
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}
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}
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\details{
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The VCF format is the standard variant call file format used in the GATK. This function reads that data in as a table for easy analysis.
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}
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\value{
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Returns a data.frame object, where each column corresponds to the columns in the VCF file.
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%% ~Describe the value returned
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%% If it is a LIST, use
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%% \item{comp1 }{Description of 'comp1'}
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%% \item{comp2 }{Description of 'comp2'}
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%% ...
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}
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\references{
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%% ~put references to the literature/web site here ~
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}
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\author{
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Kiran Garimella
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}
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\note{
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%% ~~further notes~~
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}
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\seealso{
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%% ~~objects to See Also as \code{\link{help}}, ~~~
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}
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\examples{
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vcf = gsa.read.vcf("/path/to/my/output.vcf");
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}
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\keyword{ ~kwd1 }
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