affy.subset {FEST}R Documentation

Subset of Affymetrix 500K frequency data

Description

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.

Usage

data(affy.subset)

Format

See affy.

Examples

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))

[Package FEST version 0.06 Index]