hlaFlankingSNP: SNP IDs in Flanking Region

In HIBAG: HIBAG -- HLA Genotype Imputation with Attribute Bagging

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=c("auto", "hg18", "hg19", "unknown"))

Arguments

snp.id	a vector of SNP IDs
position	a vector of positions
hla.id	the name of HLA locus
flank.bp	the size of flanking region on each side in basepair
assembly	the human genome reference: "hg19" (default), "hg18", "auto" refers to "hg19"

Details

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

Value

Return allele frequecies.

Author(s)

Xiuwen Zheng

See Also

hlaGenoSubset, hlaLociInfo

Examples

# load HLA types and SNP genotypes
data(HLA_Type_Table, package="HIBAG")
data(HapMap_CEU_Geno, package="HIBAG")

# 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)

HIBAG documentation built on May 2, 2019, 4:50 p.m.