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.
Arguments
- vcf
an imported vcf file in in a list using
readVCFor a data frame of genotypes generated usinghetTgen- 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
- cl
Optional parallel cluster object from
parallel::makeCluster(). IfNULL(default), runs serially.
Value
Returns a data frame of expected “E(Hom)” and observed “O(Hom)” homozygotes with their inbreeding coefficients.
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) # \dontrun{}
#> generating table
#>
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#> assessing per sample homozygosity
#>
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