missingGenotypeBySnpSex: Missing Counts per SNP by Sex
In amstilp/GWASTools: Tools for Genome Wide Association Studies

Description Usage Arguments Details Value Author(s) See Also Examples

For all SNPs for each sex tabulates missing SNP counts, allele counts and heterozygous counts.

1 2	missingGenotypeBySnpSex(genoData, scan.exclude = NULL, verbose = TRUE)

`genoData`	`GenotypeData` object.
`scan.exclude`	A vector containing the scan numbers of scans that are to be excluded from the total scan list.
`verbose`	Logical value specifying whether to show progress information.

This function calculates the fraction of missing genotypes for males and females for each SNP 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," "scans.per.sex," and "missing.fraction."

`missing.counts`	A matrix with one row per SNP and one column per sex containing the number of missing SNP counts for males and females, respectively.
`scans.per.sex`	A vector containing the number of males and females respectively.
`missing.fraction`	A vector containing the fraction of missing counts for each SNP, with females excluded for the Y chromosome.

Cathy Laurie, Stephanie Gogarten

GenotypeData, missingGenotypeByScanChrom

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 <- missingGenotypeBySnpSex(genoData)
close(genoData)