GWASTools (version 1.18.0)

missingGenotypeByScanChrom: Missing Counts per Scan per Chromosome

Description

This function tabulates missing genotype calls for each scan for each chromosome.

Usage

missingGenotypeByScanChrom(genoData, snp.exclude = NULL,  verbose = TRUE)

Arguments

genoData

GenotypeData object. Chromosomes are expected to be in contiguous blocks.

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.

Value

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.

Details

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.

See Also

GenotypeData, missingGenotypeBySnpSex

Examples

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)