hlaBED2Geno: Convert from PLINK BED format

In zhengxwen/HIBAG: HLA Genotype Imputation with Attribute Bagging

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 non-standard alleles (except A,G,C,T)
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; "6" for all SNPs on chromosome 6 for HLA; "19" for all SNPs on chromosome 19 for KIR
assembly	the human genome reference: "hg18", "hg19" (default), "hg38"; "auto" refers to "hg19"; "auto-silent" refers to "hg19" without any warning
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)

# Or

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

zhengxwen/HIBAG documentation built on April 16, 2024, 8:41 a.m.