hlaSNPID: Get SNP IDs and positions

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

Description

Get the information of SNP ID with or without position.

Usage

hlaSNPID(obj, type=c("RefSNP+Position", "RefSNP", "Position"))

Arguments

obj	a genotypic object of hlaSNPGenoClass, a haplotypic object of hlaSNPHaploClass, a model object of hlaAttrBagClass or a model object of hlaAttrBagObj
type	"RefSNP+Position" (by default), "RefSNP" or "Position"

Value

If type = "RefSNP+Position", return paste(obj$snp.id, obj$snp.position, sep="-"); if type = "RefSNP", return obj$snp.id; otherwise, return obj$snp.position.

Author(s)

Xiuwen Zheng

See Also

hlaGenoSwitchStrand, hlaGenoCombine

Examples

# load SNP genotypes
data(HapMap_CEU_Geno, package="HIBAG")

x <- hlaSNPID(HapMap_CEU_Geno)
head(x)

x <- hlaSNPID(HapMap_CEU_Geno, "RefSNP")
head(x)

x <- hlaSNPID(HapMap_CEU_Geno, "Position")
head(x)

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