customProDB (version 1.12.0)

Multiple_VCF: Generate shared variation dataset from multiple VCF files

Description

Load multiple vcf files and output a GRange object with SNVs present in multiple samples.

Usage

Multiple_VCF(vcfs, share_num, ...)

Arguments

vcfs

a list of GRanges object which input from multiple VCF files using function InputVcf.

share_num

Two options, percentage format or sample number.

...

additional arguments

Value

a GRange object that contains the shared variations

Details

This function allows to limit SNVs that are present in at least m out of n VCF files.

Examples

path <- system.file("extdata/vcfs", package="customProDB")
vcfFiles<- paste(path, '/', list.files(path, pattern="*vcf$"), sep='')
vcfs <- lapply(vcfFiles, function(x) InputVcf(x))
shared <- Multiple_VCF(vcfs, share_num=2)