prepareHetero {MADSEQ} | R Documentation |
given the vcf file and bed file containing targeted region, generate processed heterozygous sites for furthur analysis
prepareHetero(vcffile, target_bed, genome = "hg19", writeToFile = TRUE, destination = NULL, plot = FALSE)
vcffile |
A |
target_bed |
A |
genome |
A |
writeToFile |
|
destination |
A |
plot |
A |
If writeToFile
is set to TRUE, processed table will be
written to the destination
. Otherwise, a GRanges
object containing each of input sample will be returned.
1. The vcf file you provided need to be compressed by bgzip
2. The vcf file should contain depth and allelic depth for variants in the
FORMAT field
Yu Kong
## specify the path to the vcf.gz file for the aneuploidy sample aneuploidy_vcf=system.file("extdata","aneuploidy.vcf.gz",package="MADSEQ") target = system.file("extdata","target.bed",package="MADSEQ") ##------ if not write to file ------ aneuploidy_hetero=prepareHetero(aneuploidy_vcf,target,writeToFile=FALSE) ##------ if write to file ------ prepareHetero(aneuploidy_vcf, target,writeToFile=TRUE, destination=".")