hlaFlankingSNP {HIBAG} | R Documentation |
To get SNPs in the flanking region of a specified HLA/KIR locus.
hlaFlankingSNP(snp.id, position, locus, flank.bp=500000L, assembly="auto", pos.start=NA_integer_, pos.end=NA_integer_) hlaGenoSubsetFlank(genoobj, locus="any", flank.bp=500000L, assembly="auto")
snp.id |
a vector of SNP IDs |
genoobj |
a genotype object of |
position |
a vector of positions |
locus |
the name of HLA locus, or "any" for other genes |
flank.bp |
the size of flanking region on each side in basepair |
assembly |
the human genome reference: "hg18", "hg19" (default), "hg38"; "auto" refers to "hg19"; "auto-silent" refers to "hg19" without any warning |
pos.start |
the start position of the gene |
pos.end |
the end position of the gene |
hla.id
is "A", "B", "C", "DRB1", "DRB5", "DQA1", "DQB1", "DPB1" or
"any".
Return selected SNP IDs from snp.id
.
Xiuwen Zheng
# make a "hlaAlleleClass" object hla.id <- "A" hla <- hlaAllele(HLA_Type_Table$sample.id, H1 = HLA_Type_Table[, paste(hla.id, ".1", sep="")], H2 = HLA_Type_Table[, paste(hla.id, ".2", sep="")], locus=hla.id, assembly="hg19") # training genotypes region <- 500 # kb snpid <- hlaFlankingSNP(HapMap_CEU_Geno$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)) summary(train.geno) # or using hlaGenoSubsetFlank train.geno <- hlaGenoSubsetFlank(HapMap_CEU_Geno, hla.id, region*1000) summary(train.geno) ## customize positions snpid <- hlaFlankingSNP(HapMap_CEU_Geno$snp.id, HapMap_CEU_Geno$snp.position, "any", 500*1000, pos.start=29457816, pos.end=30450205)