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Determine per sample heterozygosity and inbreeding coefficient

Source: R/statistics.R
h.zygosity.Rd

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)

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

Value

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

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)
#> Error in eval(expr, envir, enclos): object 'vcf.file.path' not found
pp<-substr(colnames(vcf$vcf)[-c(1:9)],1,8)
#> Error in eval(expr, envir, enclos): object 'vcf' not found
hzygots<-h.zygosity(vcf,plot=TRUE,pops=pp)
#> Error in eval(expr, envir, enclos): object 'vcf' not found