callHomozygous: Call homozygous regions from sequencing data

Description Usage Arguments Value Author(s) Examples

View source: R/callHomozygous.R

Description

Function calls homozygous regions from whole genome sequencing data.

Usage

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callHomozygous(sample, chromosomes, caller = "speedseq", MA_Window = 1000, HMZ_length  = 100000, min_n_HMZ = 20)

Arguments

sample

A name of SNV sample file to be analyzed.

chromosomes

A vector of strings indicating chromosomes to be analyzed.

caller

A string indicating vcf caller. Default is "speedseq", supports "GATK"

MA_Window

A number indicating window size for moving average function. Recommended value for genome is 2000, for exome is 20. Default is 1000.

HMZ_length

Minimal length of homozygous region to be called. Default is 100000.

min_n_HMZ

Minimal number of variants necessary to call a region. Default is 20.

Value

comp1

function calls homozygous regions from whole genome sequencing data and returns them in a tab separated txt file.

Author(s)

Tomasz Stokowy

Examples

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# sample = system.file("extdata", "CoriellIndex_S1_chr19_9-10_S1.vcf.recode.vcf.gz",
#                      package = "RareVariantVis")
# callHomozygous(sample=sample, chromosomes=c("19"))

Bioconductor-mirror/RareVariantVis documentation built on May 31, 2017, 11:41 p.m.