hlaGeno2PED {HIBAG} | R Documentation |
Convert an object of hlaSNPGenoClass
to a file of
PLINK PED format.
hlaGeno2PED(geno, out.fn)
geno |
a genotype object of |
out.fn |
the file name of output ped file |
Two files ".map" and ".ped" are created.
None.
Xiuwen Zheng
# make a "hlaAlleleClass" object hla.id <- "A" hla <- hlaAllele(HLA_Type_Table$sample.id, H1 = HLA_Type_Table[, paste(hla.id, ".1", sep="")], H2 = HLA_Type_Table[, paste(hla.id, ".2", sep="")], max.resolution="4-digit", locus=hla.id, assembly="hg19") # training genotypes region <- 500 # kb snpid <- hlaFlankingSNP(HapMap_CEU_Geno$snp.id, HapMap_CEU_Geno$snp.position, hla.id, region*1000, assembly="hg19") train.geno <- hlaGenoSubset(HapMap_CEU_Geno, snp.sel = match(snpid, HapMap_CEU_Geno$snp.id)) hlaGeno2PED(train.geno, "test") # delete the temporary files unlink(c("test.map", "test.ped"), force=TRUE)