hlaFlankingSNP {HIBAG} | R Documentation

## SNP IDs or SNP genotypes in Flanking Region

### Description

To get SNPs in the flanking region of a specified HLA/KIR locus.

### Usage

    hlaFlankingSNP(snp.id, position, locus, flank.bp=500000L, assembly="auto",
        pos.start=NA_integer_, pos.end=NA_integer_)
    hlaGenoSubsetFlank(genoobj, locus="any", flank.bp=500000L, assembly="auto")

### Arguments

`snp.id` | a vector of SNP IDs
`genoobj` | a genotype object of `hlaSNPGenoClass`
`position` | a vector of positions
`locus` | the name of HLA locus, or "any" for other genes
`flank.bp` | the size of flanking region on each side in basepair
`assembly` | the human genome reference: "hg18", "hg19" (default), "hg38"; "auto" refers to "hg19"; "auto-silent" refers to "hg19" without any warning
`pos.start` | the start position of the gene
`pos.end` | the end position of the gene

### Details

`hla.id` is "A", "B", "C", "DRB1", "DRB5", "DQA1", "DQB1", "DPB1" or "any".

### Value

Return selected SNP IDs from `snp.id`.

### Author(s)

Xiuwen Zheng

### See Also

`hlaGenoSubset`, `hlaLociInfo`

### Examples

    # make a "hlaAlleleClass" object
    hla.id <- "A"
    hla <- hlaAllele(HLA_Type_Table$sample.id,
        H1 = HLA_Type_Table[, paste(hla.id, ".1", sep="")],
        H2 = HLA_Type_Table[, paste(hla.id, ".2", sep="")],
        locus=hla.id, assembly="hg19")

    # training genotypes
    region <- 500   # kb
    snpid <- hlaFlankingSNP(HapMap_CEU_Geno$snp.id, HapMap_CEU_Geno$snp.position,
        hla.id, region*1000, assembly="hg19")
    train.geno <- hlaGenoSubset(HapMap_CEU_Geno,
        snp.sel  = match(snpid, HapMap_CEU_Geno$snp.id))
    summary(train.geno)

    # or using hlaGenoSubsetFlank
    train.geno <- hlaGenoSubsetFlank(HapMap_CEU_Geno, hla.id, region*1000)
    summary(train.geno)

    ## customize positions
    snpid <- hlaFlankingSNP(HapMap_CEU_Geno$snp.id, HapMap_CEU_Geno$snp.position,
        "any", 500*1000, pos.start=29457816, pos.end=30450205)

[Package HIBAG version 1.16.0 Index]