get.miss {rCNV} | R Documentation |
Get missingness of individuals in raw vcf
Description
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)
Arguments
data |
a list containing imported vcf file using |
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 |
Value
Returns a data frame of allele depth or genotypes
Author(s)
Piyal Karunarathne
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)
[Package rCNV version 1.2.0 Index]