hlaGenoCombine: Combine two genotypic data sets into one

In zhengxwen/HIBAG: HLA Genotype Imputation with Attribute Bagging

Combine two genotypic data sets into one

Description

To combine two genotypic data sets into one dataset.

Usage

hlaGenoCombine(geno1, geno2,
    match.type=c("Position", "Pos+Allele", "RefSNP+Position", "RefSNP"),
    allele.check=TRUE, same.strand=FALSE, verbose=TRUE)

Arguments

geno1	the first genotype object of hlaSNPGenoClass
geno2	the second genotype object of hlaSNPGenoClass
match.type	"RefSNP+Position" (by default) – using both of RefSNP IDs and positions; "RefSNP" – using RefSNP IDs only; "Position" – using positions only
allele.check	if TRUE, call hlaGenoSwitchStrand to check and then switch allele pairs if needed
same.strand	TRUE assuming alleles are on the same strand (e.g., forward strand); otherwise, FALSE not assuming whether on the same strand or not
verbose	show information, if TRUE

Details

The function merges two SNP dataset geno1 and geno2, and returns a SNP dataset consisting of the SNP intersect between geno1 and geno2, and having the same SNP information (allele and position) as geno1.

Value

An object of hlaSNPGenoClass.

Author(s)

Xiuwen Zheng

See Also

hlaMakeSNPGeno, hlaGenoSubset

Examples

# import a PLINK BED file
bed.fn <- system.file("extdata", "HapMap_CEU.bed", package="HIBAG")
fam.fn <- system.file("extdata", "HapMap_CEU.fam", package="HIBAG")
bim.fn <- system.file("extdata", "HapMap_CEU.bim", package="HIBAG")
hapmap.ceu <- hlaBED2Geno(bed.fn, fam.fn, bim.fn, assembly="hg19")

# combine two datasets together
geno <- hlaGenoCombine(HapMap_CEU_Geno, hapmap.ceu)
summary(geno)

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