bambaf_from_vcf: Get BAM baf information from vcf
In zhouzilu/iCNV: Integrated Copy Number Variation detection

Description Usage Arguments Value Examples

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

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

`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 ”

void

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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.')