hlaBED2Geno: Convert from PLINK BED format

In HIBAG: HIBAG -- HLA Genotype Imputation with Attribute Bagging

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=c("auto", "hg18", "hg19", "unknown"),
	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: "hg19" (default), "hg18", "auto" refers to "hg19"
verbose	if TRUE, show information

Value

Return an object of hlaSNPGenoClass.

Author(s)

Xiuwen Zheng

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)

HIBAG documentation built on May 2, 2019, 4:50 p.m.