bambaf_from_vcf {iCNV} | R Documentation

## Get BAM baf information from vcf

### Description

If your vcf follow the format in the example, you could use this function to extract NGS baf from vcf files. Remember to load library before hands. Save 6 lists, each list has N entry. N = # of individuals (or vcf file) ngs_baf.nm: name of the bamfiles; ngs_baf.chr: the chromosome; ngs_baf.pos: the position of the variants; ngs_baf: the BAF of the variants; ngs_baf.id: the ID of the variants; filenm:the file name

### Usage

    bambaf_from_vcf(dir = ".", vcf_list, chr = NULL, projname = "")

### Arguments

`dir` | The directory to all the vcf stored; default is right in this folder. Type character. Defualt '.'
`vcf_list` | All the vcf names stored in vcf.list; could use command:"ls *.vcf > vcf.list" to generate. Type character.
`chr` | Specify the chromosome you want to generate. Must be of int from 1-22. If not specify, this function will generate all chromosomes. Defualt NULL
`projname` | Name of the project. Type character. Default ”

### Value

void

### Examples

    dir <- system.file("extdata", package="iCNV")
    bambaf_from_vcf(dir,'bam_vcf.list',projname='icnv.demo.')
    bambaf_from_vcf(dir,'bam_vcf.list',chr=22,projname='icnv.demo.')

[Package iCNV version 1.12.0 Index]