prepareHetero: prepare heterozygous sites for aneuploidy detection
given the vcf file and bed file containing targeted region, generate
processed heterozygous sites for furthur analysis
character, specify the path to the location of the
vcf.gz file of your sample. Note: the vcf file need to be compressed
bgzip. The tool is part of
can be download from http://www.htslib.org/
character, specify the path to the location of
bed file containing targeted regions.
character, specify the assembly of your genome.
Default: hg19. To see available genome assembly,
available.genomes from BSgenome package
processed table containing heterozygous sites will be written to
destination specified, the file will be named as
"sample_filtered_heterozygous.txt". If set to
GRanges object containing processed heterozygous sites
will be returned
character, specify the path to the location
where the processed heterozygous sites table will be written.
NULL, the file will be written to current working directory
writeToFile is set to TRUE, processed table will be
written to the
destination. Otherwise, a
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
## specify the path to the vcf.gz file for the aneuploidy sample
target = system.file("extdata","target.bed",package="MADSEQ")
##------ if not write to file ------
##------ if write to file ------
prepareHetero(aneuploidy_vcf, target,writeToFile=TRUE, destination=".")