hlaFlankingSNP: SNP IDs or SNP genotypes in Flanking Region

In zhengxwen/HIBAG: HLA Genotype Imputation with Attribute Bagging

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.mid=NA_integer_)
hlaGenoSubsetFlank(genoobj, locus="any", flank.bp=500000L, assembly="auto",
    pos.mid=NA_integer_)

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 and using pos.mid
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.mid	the middle position of the flanking region

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.mid=29954010)

zhengxwen/HIBAG documentation built on Nov. 19, 2024, 1:01 p.m.