hlaBED2Geno {HIBAG} | R Documentation

## 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; "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)

[Package HIBAG version 1.18.1 Index]