R: Allele switching

hlaGenoSwitchStrand {HIBAG}

R Documentation

Allele switching

Description

Determine the ordered pair of A and B alleles, using the allele information provided by template.

Usage

hlaGenoSwitchStrand(target, template,
    match.type=c("RefSNP+Position", "RefSNP", "Position"),
    same.strand=FALSE, verbose=TRUE)

Arguments

`target`	an object of `hlaSNPGenoClass`
`template`	a genotypic object of `hlaSNPGenoClass`, a model object of `hlaAttrBagClass` or a model object of `hlaAttrBagObj`
`match.type`	`"RefSNP+Position"` (by default) – using both of RefSNP IDs and positions; `"RefSNP"` – using RefSNP IDs only; `"Position"` – using positions only
`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 A/B pairs of target are determined using the information from template.

Value

Return a hlaSNPGenoClass object consisting of the SNP intersect between target and template.

Author(s)

Xiuwen Zheng

Examples

summary(HapMap_CEU_Geno)
# A/C A/G C/T G/T 
# 136 655 632 141 

# 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")
summary(hapmap.ceu)
# A/C  A/G  A/T  C/G  C/T  G/T
# 332 1567   64  111 1510  348

# combine two datasets together
geno <- hlaGenoSwitchStrand(HapMap_CEU_Geno, hapmap.ceu)
summary(geno)
# There are 1564 SNPs in common.
# The allele pairs of 763 SNPs need to be switched.
# A/C A/G C/T G/T
# 104 505 496 109

[Package HIBAG version 1.24.0 Index]