R: Combine two genotypic data sets into one

hlaGenoCombine {HIBAG}

R Documentation

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

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

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)

[Package HIBAG version 1.22.0 Index]