Multiple_VCF: Generate shared variation dataset from multiple VCF files

In customProDB: Generate customized protein database from NGS data, with a focus on RNA-Seq data, for proteomics search

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

Details

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

Value

a GRange object that contains the shared variations

Author(s)

Xiaojing Wang

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)

customProDB documentation built on Nov. 8, 2020, 8:06 p.m.