isSNV: Determine if variants in a VCF object are SNPs

In seandavi/MutationTools: What the package does (short line)

Description

Returns TRUE for variants that are SNVs and FALSE otherwise. For variants with multiple ALT alleles, only the FIRST is used.

Usage

isSNV(vcf)

Arguments

VCF	an object inheriting from the VCF class

Value

logical vector with the same length as vcf

See Also

VCF-class

Examples

library(VariantAnnotation)
fl <- system.file("extdata", "chr22.vcf.gz", package="VariantAnnotation")
param <- ScanVcfParam(fixed="ALT", geno=c("GT", "GL"), info=c("LDAF"))
vcf = readVcf(fl,"hg19",param=param)
table(isSNV(vcf))

seandavi/MutationTools documentation built on May 29, 2019, 4:32 p.m.