get.miss: Get missingness of individuals in raw vcf

In rCNV: Detect Copy Number Variants from SNPs Data

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
)

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

Value

Returns a data frame of allele depth or genotypes

Author(s)

Piyal Karunarathne

Examples

## Not run: 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)
## End(Not run)

rCNV documentation built on Sept. 30, 2024, 9:39 a.m.