affy.subset {FEST} | R Documentation |
A subset of the allele frequency data from the Affymetrix 500K chip derived from the HapMap data. It contains frequency information of 100 markers for all 22 autosomal chromosomes.
data(affy.subset)
See affy
.
data(affy.subset) ## Average frequencies for chromosome 1: f <- apply(affy.subset[[1]][,-c(1,2)],2,mean) print(f) ## Minor allele frequency for chromosome 1 maf1 <- pmin(affy.subset[[1]][,3], affy.subset[[1]][,4]) ## Empirical cumulative distribution function plot(ecdf(maf1), xlim=c(0,0.5)) ## Some statistics stat <- c(length(maf1), mean(maf1>0.01), mean(maf1>0.02), mean(maf1>0.05))