A function to get the percentage of missing data of snps per SNP and per sample
Usage
get.miss(
data,
type = c("samples", "snps"),
plot = TRUE,
verbose = TRUE,
parallel = FALSE
)Arguments
- data
a list containing imported vcf file using
readVCFor genotype table generated usinghetTgen- type
character. Missing percentages per sample “samples” or per SNP “snps”, default both
- plot
logical. Whether to plot the missingness density with ninety five percent quantile
- verbose
logical. Whether to show progress
- parallel
logical. whether to parallelize the process
Examples
vcf.file.path <- paste0(path.package("rCNV"), "/example.raw.vcf.gz")
vcf <- readVCF(vcf.file.path=vcf.file.path)
missing<-get.miss(vcf,plot=TRUE)
#> generating table
#>
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#> assessing % missing samples
#>
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#> assessing % missing sites
#>
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