prepareHetero: prepare heterozygous sites for aneuploidy detection

In ykong2/MADSEQ: Mosaic Aneuploidy Detection and Quantification using Massive Parallel Sequencing Data

Description

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

Usage

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

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
plot	A Boolean Default: FALSE. If TRUE, A plot showing AAF before and after filtering for problematic regions will be generated

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

## 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=".")

ykong2/MADSEQ documentation built on May 4, 2019, 5:30 p.m.