affy {FEST}R Documentation

Affymetrix 500K frequency data

Description

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.

Usage

## download file from 'http://folk.uio.no/thoree/FEST/affy.RData'

Format

List of length 22 where element i (affy[[i]]) is a data frame with the following columns:

SNP
Name of SNP
cM
Distance in centi Morgan
A
Frequency of allele A
C
Frequency of allele C

Source

http://www.stats.ox.ac.uk/~marchini/software/gwas/chiamo.html

Examples

## 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))

[Package FEST version 0.06 Index]