HIBAG (version 1.8.3)

hlaFlankingSNP: SNP IDs in Flanking Region

Description

To select SNPs in the flanking region of a specified HLA locus.

Usage

hlaFlankingSNP(snp.id, position, hla.id, flank.bp=500*1000, assembly="auto", pos.start=NA_integer_, pos.end=NA_integer_)

Arguments

snp.id

a vector of SNP IDs

position

a vector of positions

hla.id

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), "hg20"; "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

Value

Return selected SNP IDs from snp.id.

Details

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

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$snp.id),
    samp.sel = match(hla$training$value$sample.id, HapMap_CEU_Geno$sample.id))
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)