GWASTools (version 1.18.0)

alleleFrequency: Allelic frequency

Description

Calculates the frequency of the A allele over the specifed scans.

Usage

alleleFrequency(genoData, scan.exclude, verbose = TRUE)

Arguments

genoData

GenotypeData object.

scan.exclude

Integer vector with IDs of scans to exclude.

verbose

Logical value specifying whether to show progress information.

Value

A matrix with a row for each SNP. Columns "M" for males, "F" for females, and "all" for all scans give frequencies of the A allele. Sample size for males, females, and all is returned as "n.M", "n.F", and "n", respectively. "MAF" is the minor allele frequency over all scans.

Details

Counts male heterozygotes on the X and Y chromosomes as missing values, and any genotype for females on the Y chromosome as missing values. A "sex" variable must be present in the scan annotation slot of genoData.

Samples with missing sex are included in the allele counts for "all" and "MAF" for autosomes, but not for sex chromosomes.

See Also

GenotypeData

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)

afreq <- alleleFrequency(genoData, scan.exclude=(illuminaScanADF$race != "CEU"))
close(genoData)