hetBySnpSex {GWASTools} | R Documentation |
This function calculates the percent of heterozygous genotypes for males and females for each SNP.
hetBySnpSex(genoData, scan.exclude = NULL, verbose = TRUE)
genoData |
|
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
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)