Description Usage Arguments Details Value Author(s) See Also Examples
Calculates the frequency of the A allele over the specifed scans.
1 2 | alleleFrequency(genoData, scan.exclude,
verbose = TRUE)
|
genoData |
|
scan.exclude |
Integer vector with IDs of scans to exclude. |
verbose |
Logical value specifying whether to show progress information. |
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.
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.
Cathy Laurie, Stephanie Gogarten
1 2 3 4 5 6 7 8 9 10 | 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)
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