hetBySnpSex: Heterozygosity by SNP and sex
In GWASTools: Tools for Genome Wide Association Studies

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

This function calculates the percent of heterozygous genotypes for males and females for each SNP.

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

`genoData`	`GenotypeData` object
`scan.exclude`	An integer vector containing the id's of scans to be excluded.
`verbose`	Logical value specifying whether to show progress information.

This function calculates the percent of heterozygous genotypes for males and females for each SNP given in genoData. A "sex" variable must be present in the scan annotation slot of genoData.

The result is a matrix containing the heterozygosity rates with snps as rows and 2 columns ("M" for males and "F" for females).

Cathy Laurie

GenotypeData, hetByScanChrom

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)

het <- hetBySnpSex(genoData)
close(genoData)