rCNV (version 1.3.0)

get.miss: 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,
  parallel = FALSE
)

Value

Returns a data frame of allele depth or genotypes

Arguments

data

a list containing imported vcf file using readVCF or genotype table generated using hetTgen

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

Author

Piyal Karunarathne

Examples

if (FALSE) 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)