HIBAG (version 1.8.3)

hlaAllele: A list of HLA types

Description

Return an object of hlaAlleleClass, which contains HLA types.

Usage

hlaAllele(sample.id, H1, H2, max.resolution="", locus="any", assembly="auto", locus.pos.start=NA, locus.pos.end=NA, prob=NULL, na.rm=TRUE)

Arguments

sample.id

sample IDs

H1

a vector of HLA alleles

H2

a vector of HLA alleles

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

locus

the name of HLA locus: "A", "B", "C", "DRB1", "DRB5", "DQA1", "DQB1", "DPB1", or "any", where "any" indicates any other multiallelic locus

assembly

the human genome reference: "hg18", "hg19" (default), "hg20"; "auto" refers to "hg19"; "auto-silent" refers to "hg19" without any warning

locus.pos.start

the starting position in basepair

locus.pos.end

the end position in basepair

prob

the probabilities assigned to the samples

na.rm

if TRUE, remove the samples without valid HLA types

Value

Return a hlaAlleleClass object, and it is a list:

locus

HLA locus

pos.start

the starting position in basepair

pos.end

the end position in basepair

value

a data frame

assembly

the human genome reference, such like "hg19"

The component value includes:

sample.id

sample ID

allele1

HLA allele

allele2

HLA allele

prob

the posterior probability

Details

The format of H1 and H2 is "allele group : different protein : synonymous mutations in exons : synonymous mutations in introns"L, where the suffix L is express level (N, null; L, low; S, secreted; A, aberrant; Q: questionable). For example, "44:02:01:02L". If max.resolution is specified, the HLA alleles will be trimmed with a possible maximum resolution.

See Also

hlaAlleleDigit, hlaAlleleSubset

Examples

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)


# encode other loci
hlaAllele("HD0010", "1", "2", locus="NewLocus")