rCNV (version 1.3.0)

h.zygosity: Determine per sample heterozygosity and inbreeding coefficient

Description

This function will calculate the heterozygosity on a per-sample basis from vcf files (snps), and most importantly inbreeding coefficient which is used to filter out the samples with bad mapping quality.

Usage

h.zygosity(vcf, plot = FALSE, pops = NA, verbose = TRUE, parallel = FALSE)

Value

Returns a data frame of expected “E(Hom)” and observed “O(Hom)” homozygotes with their inbreeding coefficients.

Arguments

vcf

an imported vcf file in in a list using readVCF or a data frame of genotypes generated using hetTgen

plot

logical. Whether to plot a boxplot of inbreeding coefficients for populations. A list of populations must be provided

pops

character. A list of population names with the same length and order as the number of samples in the vcf

verbose

logical. Show progress

parallel

logical. Parallelize the process

Author

Piyal Karunarathne, Pascal Milesi, Klaus Schliep

Examples

if (FALSE) vcf.file.path <- paste0(path.package("rCNV"), "/example.raw.vcf.gz")
vcf <- readVCF(vcf.file.path=vcf.file.path)
pp<-substr(colnames(vcf$vcf)[-c(1:9)],1,8)
hzygots<-h.zygosity(vcf,plot=TRUE,pops=pp)