hlaGenoCombine: Combine two genotypic data sets into one
In HIBAG: 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, hlaMakeSNPHaplo, hlaHaploSubset, hlaGenoSubset

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

# 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)