InputVcf: Generate a list of GRanges objects from a VCF file.

In chambm/customProDB: Generate customized protein databases from NGS data for proteomics search

Description

The InputVcf() function generates a list of GRanges object from a single VCF file.

Usage

InputVcf(vcfFile, ...)

Arguments

vcfFile	a character contains the path and name of a VCF file
...	additional arguments

Details

Read all fields in a VCF file into GRanges object.

Value

a list of GRanges object containing a representation of data from the VCF file

Author(s)

Xiaojing Wang

Examples

## multiple samples in one VCF file

vcffile <- system.file("extdata", "test_mul.vcf", package="customProDB")
vcfs <- InputVcf(vcffile)
length(vcfs)

## single sample

vcffile <- system.file("extdata/vcfs", "test1.vcf", package="customProDB")
vcf <- InputVcf(vcffile)
length(vcf)

chambm/customProDB documentation built on May 31, 2019, 12:08 p.m.