hlaGenoSwitchStrand {HIBAG} | R Documentation

## Allele switching

### Description

Determine the ordered pair of A and B alleles, using the allele information provided by `template`.

### Usage

    hlaGenoSwitchStrand(target, template,
        match.type=c("RefSNP+Position", "RefSNP", "Position"),
        same.strand=FALSE, verbose=TRUE)

### Arguments

`target` | an object of `hlaSNPGenoClass`
`template` | a genotypic object of `hlaSNPGenoClass`, a model object of `hlaAttrBagClass` or a model object of `hlaAttrBagObj`
`match.type` | `"RefSNP+Position"` (by default) – using both of RefSNP IDs and positions; `"RefSNP"` – using RefSNP IDs only; `"Position"` – using positions only
`same.strand` | `TRUE` assuming alleles are on the same strand (e.g., forward strand); otherwise, `FALSE` not assuming whether on the same strand or not
`verbose` | show information, if TRUE

### Details

The A/B pairs of `target` are determined using the information from `template`.

### Value

Return a `hlaSNPGenoClass` object consisting of the SNP intersect between `target` and `template`.

### Author(s)

Xiuwen Zheng

### See Also

`hlaMakeSNPGeno`, `hlaGenoSubset`

### Examples

    summary(HapMap_CEU_Geno)
    # A/C A/G C/T G/T
    # 136 655 632 141

    # 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)
    # A/C  A/G  A/T  C/G  C/T  G/T
    # 332 1567   64  111 1510  348

    # combine two datasets together
    geno <- hlaGenoSwitchStrand(HapMap_CEU_Geno, hapmap.ceu)
    summary(geno)
    # There are 1564 SNPs in common.
    # The allele pairs of 763 SNPs need to be switched.
    # A/C A/G C/T G/T
    # 104 505 496 109

[Package HIBAG version 1.16.0 Index]