alleleFrequency: Allelic frequency

In smgogarten/GWASTools: Tools for Genome Wide Association Studies

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.

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.

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.

Author(s)

Cathy Laurie, Stephanie Gogarten

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)

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