bambaf_from_vcf {iCNV} | R Documentation |
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
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
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.')