hlaUniqueAllele: Get unique HLA alleles

In zhengxwen/HIBAG: HLA Genotype Imputation with Attribute Bagging

Get unique HLA alleles

Description

Get unique HLA alleles, which are in ascending order.

Usage

hlaUniqueAllele(hla, all=NA)

Arguments

hla	character-type HLA alleles, a hlaAlleleClass object, a link{hlaAttrBagClass} object, or a link{hlaAttrBagObj} object
all	when hla is a hlaAlleleClass object and all=TRUE, return all HLA alleles if hla$dosage or hla$postprob exists; otherwise, only return the alleles in hla$value

Details

Each HLA allele name has a unique number corresponding to up to four sets of digits separated by colons. The name designation depends on the sequence of the allele and that of its nearest relative. The digits before the first colon describe the type, which often corresponds to the serological antigen carried by an allotype. The next set of digits are used to list the subtypes, numbers being assigned in the order in which DNA sequences have been determined. Alleles whose numbers differ in the two sets of digits must differ in one or more nucleotide substitutions that change the amino acid sequence of the encoded protein. Alleles that differ only by synonymous nucleotide substitutions (also called silent or non-coding substitutions) within the coding sequence are distinguished by the use of the third set of digits. Alleles that only differ by sequence polymorphisms in the introns or in the 5' or 3' untranslated regions that flank the exons and introns are distinguished by the use of the fourth set of digits.

In addition to the unique allele number there are additional optional suffixes that may be added to an allele to indicate its expression status. Alleles that have been shown not to be expressed, 'Null' alleles have been given the suffix 'N'. Those alleles which have been shown to be alternatively expressed may have the suffix 'L', 'S', 'C', 'A' or 'Q'.

http://hla.alleles.org/nomenclature/index.html

Value

Return a character vector of HLA alleles

Author(s)

Xiuwen Zheng

See Also

hlaAllele, hlaAlleleDigit

Examples

# 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)
hlaUniqueAllele(hla)

hlaUniqueAllele(c("01", "01:03", "01:01", "03:05", "03:01G",
    "03:05P", "03:104:01", "104:01"))

zhengxwen/HIBAG documentation built on Nov. 19, 2024, 1:01 p.m.