readBIM {plinkFile}

Read BIM file

Description

Get variant meta-data form the bim file of a PLINK1 BED fileset.

Usage

readBIM(bim, vfr = NULL, vto = NULL)

Arguments

bim

prefix or name of a PLINK file.

vfr

variant-wise, from where to read? (index/proportion, def=1).

vto

varinat-wise, to where then stop? (index/proportion, def=P).

Details

There are six columns in a bim file

• chr: chromosme of the variant

• vid: variant id, such as an RS number;

• cmg: position by centimorgan;

• bps: position by basepairs;

• al1: allele 1, the one counted as dosage.

• al2: allele 2.

Value

data frame of variants, loaded from BIM.

Examples

bed <- file.path(system.file("extdata", package="plinkFile"), "000.bed")
bim <- readBIM(bed, 20, 30)
bim