missingGenotypeByScanChrom {GWASTools} | R Documentation |
This function tabulates missing genotype calls for each scan for each chromosome.
missingGenotypeByScanChrom(genoData, snp.exclude = NULL, verbose = TRUE)
genoData |
|
snp.exclude |
A vector of IDs corresponding to the SNPs that should be excluded from the overall missing count. |
verbose |
Logical value specifying whether to show progress information. |
This function calculates the percent of missing genotypes in each chromosome of each scan given in genoData
.
A "sex" variable must be present in the scan
annotation slot of genoData
.
This function returns a list with three components: "missing.counts," "snps.per.chr", and "missing.fraction."
missing.counts |
A matrix with rows corresponding to the scans and columns indicating unique chromosomes containing the number of missing SNP's for each scan and chromosome. |
snps.per.chr |
A vector containing the number of non-excluded SNPs for each chromosome. |
missing.fraction |
A vector containing the fraction of missing counts for each scan over all chromosomes, excluding the Y chromosome for females. |
Cathy Laurie
GenotypeData
, missingGenotypeBySnpSex
library(GWASdata) file <- system.file("extdata", "illumina_geno.gds", package="GWASdata") gds <- GdsGenotypeReader(file) # need scan annotation with sex data(illuminaScanADF) genoData <- GenotypeData(gds, scanAnnot=illuminaScanADF) missingRate <- missingGenotypeByScanChrom(genoData) close(genoData)