scanBED: Scan genotypes in PLINK BED(s)

Description

Go through a BED file set and visit one variant at a time. This is meant for out-of-memory screening of huge genotype, such as a GWAS study.

Usage

scanBED(pfx, FUN, ..., simplify = TRUE)

Value

an array with each row corresponding to a variant if simplify is set to TRUE; otherwise, a list with each element corresponding to a variant is returned.

A context vaiable ".i" is assigned to the environment of FUN, therefore, one can access the index of variant current being processed from within the body of FUN.

Arguments

pfx: prefix of PLINK BED.
FUN: the function to process each variant.
...: additional argument to pass to FUN.
simplify: TRUE to simplify the result as an array.

Details

To read an entire BED into a R matrix, see readBED instead.

A BED (binary biallelic genotype table) is comprised of three files (usually) sharing identical prefix:

pfx.fam: table of N typed individuals
pfx.bim: table of P typed genomic variants (i.e., SNPs);
pfx.bed: genotype matrix of N rows and P columns stored in condensed binary format.

The three files are commonly referred by their common prefix, e.g.:

chrX.bed, chrX.fam, and chrX.bim, are jointly specified by "chrX".

Examples

Run this code

pfx <- file.path(system.file("extdata", package="plinkFile"), "000")
ret <- scanBED(pfx, function(g)
{
    af <- mean(g, na.rm=TRUE) / 2
    maf <- min(af, 1 - af)
    c(idx=.i, mu=mean(g, na.rm=TRUE), maf=maf, nas=sum(is.na(g)))
})
print(ret[1:5, ])