affy {FEST} | R Documentation |
Allele frequency data from the Affymetrix 500K chip derived from the
HapMap data. It contains frequency information
for all 22 autosomal chromosomes.
See also affy.subset
.
## download file from 'http://folk.uio.no/thoree/FEST/affy.RData'
List of length 22 where element i (affy[[i]]) is a data frame with the following columns:
SNP
cM
A
C
http://www.stats.ox.ac.uk/~marchini/software/gwas/chiamo.html
## download file from 'http://folk.uio.no/thoree/FEST/affy.RData' ## Not run: load("affy.RData") ## Average frequencies for chromosome 1: ## Not run: f <- apply(affy[[1]][,-c(1,2)],2,mean) ## Not run: print(f) ## Minor allele frequency for chromosome 1 ## Not run: maf1 <- pmin(affy[[1]][,3], affy[[1]][,4]) ## Empirical cumulative distribution function ## Not run: plot(ecdf(maf1), xlim=c(0,0.5)) ## Some statistics ## Not run: stat <- c(length(maf1), mean(maf1>0.01), mean(maf1>0.02), mean(maf1>0.05))