HIBAG (version 1.8.3)

hlaGenoCombine: Combine two genotypic data sets into one

Description

To combine two genotypic data sets into one dataset.

Usage

hlaGenoCombine(geno1, geno2, match.type=c("RefSNP+Position", "RefSNP", "Position"), 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

Value

An object of hlaSNPGenoClass.

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.

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)