gtVcf2genoClasses: Parse VCF
In timflutre/rutilstimflutre: Timothee Flutre's personal R code
gtVcf2genoClasses R Documentation
Parse VCF
Description
Return a matrix of genotypes for SNPs (with possibly multiple alternative alleles).
Phasing information is ignored.
With help from Martin Morgan.
Usage
gtVcf2genoClasses(vcf, na.string = NA, single.alt = TRUE)
Arguments
vcf
CollapsedVCF (see pkg VariantAnnotation)
na.string
a symbol to indicate missing genotypes (e.g. NA, "NN", "–", etc)
single.alt
if TRUE, only records with a single 'alt' are kept
Value
matrix with variants in rows and samples in columns
Author(s)
Gautier Sarah, Timothee Flutre
See Also
vcf2genoClasses, gtVcf2dose
timflutre/rutilstimflutre documentation built on Feb. 7, 2024, 8:17 a.m.
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| gtVcf2genoClasses | R Documentation |
Parse VCF
Description
Return a matrix of genotypes for SNPs (with possibly multiple alternative alleles). Phasing information is ignored. With help from Martin Morgan.
Usage
gtVcf2genoClasses(vcf, na.string = NA, single.alt = TRUE)
Arguments
vcf |
CollapsedVCF (see pkg VariantAnnotation) |
na.string |
a symbol to indicate missing genotypes (e.g. NA, "NN", "–", etc) |
single.alt |
if TRUE, only records with a single 'alt' are kept |
Value
matrix with variants in rows and samples in columns
Author(s)
Gautier Sarah, Timothee Flutre
See Also
vcf2genoClasses, gtVcf2dose
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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