HIBAG (version 1.8.3)

hlaBED2Geno: Convert from PLINK BED format

Description

To convert a PLINK BED file to an object of hlaSNPGenoClass.

Usage

hlaBED2Geno(bed.fn, fam.fn, bim.fn, rm.invalid.allele=FALSE, import.chr="xMHC", assembly="auto", verbose=TRUE)

Arguments

bed.fn

binary file, genotype information

fam.fn

family, individual information, etc

bim.fn

extended MAP file: two extra cols = allele names

rm.invalid.allele

if TRUE, remove SNPs with invalid alleles

import.chr

the chromosome, "1" .. "22", "X", "Y", "XY", "MT", "xMHC", or "", where "xMHC" implies the extended MHC on chromosome 6, and "" for all SNPs

assembly

the human genome reference: "hg18", "hg19" (default), "hg20"; "auto" refers to "hg19"; "auto-silent" refers to "hg19" without any warning

verbose

if TRUE, show information

Value

Return an object of hlaSNPGenoClass.

See Also

hlaGeno2PED, hlaGDS2Geno

Examples

# Import a PLINK BED file
bed.fn <- system.file("extdata", "HapMap_CEU.bed", package="HIBAG")
fam.fn <- system.file("extdata", "HapMap_CEU.fam", package="HIBAG")
bim.fn <- system.file("extdata", "HapMap_CEU.bim", package="HIBAG")

hapmap.ceu <- hlaBED2Geno(bed.fn, fam.fn, bim.fn, assembly="hg19")
summary(hapmap.ceu)

# Or

hapmap.ceu <- hlaBED2Geno(bed.fn, fam.fn, bim.fn, assembly="hg19",
    rm.invalid.allele=TRUE, import.chr="6")
summary(hapmap.ceu)