hlaSNPID: Get SNP IDs and positions

In zhengxwen/HIBAG: HLA Genotype Imputation with Attribute Bagging

Get SNP IDs and positions

Description

Get the information of SNP ID with or without position.

Usage

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

Arguments

obj	a genotypic object of hlaSNPGenoClass, 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$snp.id; if type = "Position", return obj$snp.position; if type = "Pos+Allele", return paste(obj$snp.position, obj$snp.allele, sep="-").

Author(s)

Xiuwen Zheng

See Also

hlaGenoSwitchStrand, hlaGenoCombine

Examples

x <- hlaSNPID(HapMap_CEU_Geno)
head(x)

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

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

zhengxwen/HIBAG documentation built on Nov. 24, 2024, 5:24 a.m.