Determine per sample heterozygosity and inbreeding coefficient

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)

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

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) # \dontrun{}
#> Error in eval(expr, envir, enclos): object 'vcf' not found