Get missingness of individuals in raw vcf

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

Piyal Karunarathne

Examples

if (FALSE) vcf.file.path <- paste0(path.package("rCNV"), "/example.raw.vcf.gz")
vcf <- readVCF(vcf.file.path=vcf.file.path)
#> Error: object 'vcf.file.path' not found
missing<-get.miss(vcf,plot=TRUE) # \dontrun{}
#> Error: object 'vcf' not found