hetBySnpSex: Heterozygosity by SNP and sex

In smgogarten/GWASTools: Tools for Genome Wide Association Studies

Heterozygosity by SNP and sex

Description

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

Usage

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

Arguments

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.

Details

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.

Value

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

Author(s)

Cathy Laurie

See Also

GenotypeData, hetByScanChrom

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)

het <- hetBySnpSex(genoData)
close(genoData)

smgogarten/GWASTools documentation built on July 4, 2023, 2:32 a.m.