hlaGenoSwitchStrand: Allele flipping if needed

In zhengxwen/HIBAG: HLA Genotype Imputation with Attribute Bagging

Allele flipping if needed

Description

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

Usage

hlaGenoSwitchStrand(target, template,
    match.type=c("Position", "Pos+Allele", "RefSNP+Position", "RefSNP"),
    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

See Also

hlaMakeSNPGeno, hlaGenoSubset

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

zhengxwen/HIBAG documentation built on Nov. 24, 2024, 5:24 a.m.