hlaGenoCombine: Combine two genotypic data sets into one
In HIBAG: HLA Genotype Imputation with Attribute Bagging

Description Usage Arguments Details Value Author(s) See Also Examples

To combine two genotypic data sets into one dataset.

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

`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

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.

An object of hlaSNPGenoClass.

Xiuwen Zheng

hlaMakeSNPGeno, hlaGenoSubset

# 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)