prepare heterozygous sites for aneuploidy detection

Description

given the vcf file and bed file containing targeted region, generate processed heterozygous sites for furthur analysis

Usage

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prepareHetero(vcffile, target_bed, genome = "hg19", writeToFile = TRUE,
  destination = NULL)

Arguments

vcffile

A character, specify the path to the location of the vcf.gz file of your sample. Note: the vcf file need to be compressed by bgzip. The tool is part of tabix package, can be download from http://www.htslib.org/

target_bed

A character, specify the path to the location of bed file containing targeted regions.

genome

A character, specify the assembly of your genome. Default: hg19. To see available genome assembly, use available.genomes from BSgenome package

writeToFile

Boolean Default: TRUE. If TRUE, processed table containing heterozygous sites will be written to destination specified, the file will be named as "sample_filtered_heterozygous.txt". If set to FALSE, a GRanges object containing processed heterozygous sites will be returned

destination

A character, specify the path to the location where the processed heterozygous sites table will be written. Default: NULL, the file will be written to current working directory

Value

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.

Note

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

Author(s)

Yu Kong

See Also

runMadSeq

Examples

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## 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=".")