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
readVCF
or 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
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
#>
|
| | 0%
|
|===== | 10%
|
| | 0%
|
|========== | 20%
|
| | 0%
|
|=============== | 30%
|
| | 0%
|
|==================== | 40%
|
| | 0%
|
|========================= | 50%
|
| | 0%
|
|============================== | 60%
|
| | 0%
|
|=================================== | 70%
|
| | 0%
|
|======================================== | 80%
|
| | 0%
|
|============================================= | 90%
|
| | 0%
|
|==================================================| 100%