hlaGenoSwitchStrand {HIBAG} | R Documentation |
Determine the ordered pair of A and B alleles, using the allele information
provided by template
.
hlaGenoSwitchStrand(target, template, match.type=c("Position", "Pos+Allele", "RefSNP+Position", "RefSNP"), same.strand=FALSE, verbose=TRUE)
target |
an object of |
template |
a genotypic object of |
match.type |
|
same.strand |
|
verbose |
show information, if TRUE |
The A/B pairs of target
are determined using the information from
template
.
Return a hlaSNPGenoClass
object consisting of the SNP
intersect between target
and template
.
Xiuwen Zheng
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