Description Usage Arguments Details Value Author(s) See Also Examples
Trim HLA alleles to specified width.
1 | hlaAlleleDigit(obj, max.resolution="4-digit", rm.suffix=FALSE)
|
obj |
should be a |
max.resolution |
"2-digit", "4-digit", "6-digit", "8-digit", "allele", "protein", "2", "4", "6", "8", "full" or "": "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
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 | # load HLA types and SNP genotypes
data(HLA_Type_Table, package="HIBAG")
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)
|
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