hlaAlleleDigit {HIBAG} | R Documentation |
Trim HLA alleles to specified width.
hlaAlleleDigit(obj, max.resolution="4-digit", rm.suffix=FALSE)
obj |
should be a |
max.resolution |
"2-digit", "1-field", "4-digit", "2-field", "6-digit", "3-field", "8-digit", "4-field", "allele", "protein", "full", "", "none": "allele" = "2-digit"; "protein" = "4-digit"; "full" and "" indicating no limit on resolution |
rm.suffix |
whether remove the suffix, e.g., for "01:22N", "N" is a suffix |
Either HLAtypes
or H1
H2
should be specified. The
format of HLAtypes
is "allele 1 / allele 2", e.g., "0512/0102". If
max.resolution
is specified, the HLA alleles will be trimmed with the
maximum resolution.
Return a hlaAlleleClass
object if obj
is
hlaAlleleClass
-type, or characters if obj
is
character-type.
Xiuwen Zheng
head(HLA_Type_Table) dim(HLA_Type_Table) # 60 13 # 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") summary(hla) hla2 <- hlaAlleleDigit(hla, "2-digit") summary(hla2)