HIBAG (version 1.8.3)

hlaConvSequence: Conversion From HLA Alleles to Amino Acid Sequences

Description

Convert (P-coded or G-coded) HLA alleles to amino acid sequences.

Usage

hlaConvSequence(hla=character(), locus=NULL, method=c("protein", "protein_reference"), code=c("exact", "P.code", "G.code", "P.code.merge", "G.code.merge"), region=c("auto", "all", "P.code", "G.code"), release=c("v3.22.0"), replace=NULL)

Arguments

hla

characters, or an object of hlaAlleleClass, at least 4-digit or 2-field (P-coded) HLA alleles

locus

"A", "B", "C", "DRB1", "DQA1", "DQB1", "DPB1" or "DPA1"

method

"protein": returns protein sequence alignments, "protein_reference": returns the protein sequence alignment reference

code

"exact": requires full resolution; "P.code": allows ambiguous alleles according to P code; "G.code": allows ambiguous alleles according to G code; "P.code.merge" and "G.code.merge" merge multiple ambiguous allele sequences by masking unknown or ambiguous amino acid an asterisk

region

"all": returns all amino acid or nucleotide sequences; "P.code", "G.code": returns the exon 2 and 3 for HLA class I, and the exon 2 for HLA class II alleles; "auto": region="all" if code=="exact", region="P.code" if code=="P.code"|"P.code.merge", region="G.code" if code=="G.code"|"G.code.merge"

release

"v3.22.0" -- IPD-IMGT/HLA 3.22.0 database (2015-10-07)

replace

NULL, or a character vector, like c("09:02"="107:01"), any "09:02" will be replaced by "107:01"

Value

Return an object of hlaAASeqClass or a list of characters. NULL or NA in the list indicates no matching.

Details

The P or G codes for reporting of ambiguous allele typings can be found: http://hla.alleles.org/alleles/p_groups.html or http://hla.alleles.org/alleles/g_groups.html. The protein sequences for each HLA alleles could be found: http://hla.alleles.org/alleles/text_index.html.

Due to allelic ambiguity, multiple alleles are assigned to a 2-field P-coded allele or 3-field G-coded allele. For HLA Class I alleles, identity in the 'antigen binding domains' is based on identical protein sequences as encoded by exons 2 and 3. For HLA Class II alleles this is based on identical protein sequences as encoded by exon 2. P codes and G codes encode the same protein sequence for the peptide binding domains (exon 2 and 3 for HLA class I and exon 2 only for HLA class II alleles).

1. the sequence is displayed as a hyphen "-" where it is identical to the reference.

2. an insertion or deletion is represented by a period ".".

3. an unknown or ambiguous position in the alignment is represented by an asterisk "*".

4. a capital X is used for the 'stop' codons in protein alignments.

http://hla.alleles.org/alleles/formats.html

HLA class I and II sequence alignments (Text Index): http://hla.alleles.org/alleles/text_index.html

WARNING: if you are not familiar with HLA nomenclature, you might consult with the package author or anyone who is familiar with HLA sequence alignments.

References

The licence and disclaimer of distributed HLA data: Creative Commons Attribution-NoDerivs Licence (http://hla.alleles.org/terms.html).

Robinson J, Halliwell JA, Hayhurst JH, Flicek P, Parham P, Marsh SGE: The IPD and IMGT/HLA database: allele variant databases. Nucleic Acids Research. 2015 43:D423-431

Robinson J, Malik A, Parham P, Bodmer JG, Marsh SGE: IMGT/HLA - a sequence database for the human major histocompatibility complex. Tissue Antigens. 2000 55:280-7

See Also

hlaAlleleSubset

Examples

hlaConvSequence(locus="A", method="protein_reference")
hlaConvSequence(c("01:01", "02:02", "01:01:01G", "01:01:01:01", "07"),
    locus="A")
hlaConvSequence(c("01:01", "02:02", "01:01:01G", "01:01:01:01", "07"),
    locus="A", code="P.code")
hlaConvSequence(c("01:01", "02:02", "01:01:01G", "01:01:01:01", "07"),
    locus="A", code="P.code.merge")


hlaConvSequence(locus="DPB1", method="protein_reference")
hlaConvSequence(c("09:01", "09:02"), locus="DPB1", replace=c("09:02"="107:01"))
hlaConvSequence(c("09:01", "09:02"), locus="DPB1", code="P.code",
    replace=c("09:02"="107:01"))
hlaConvSequence(c("09:01", "09:02"), locus="DPB1", code="P.code.merge",
    replace=c("09:02"="107:01"))


hlaConvSequence(locus="DQB1", method="protein_reference")
hlaConvSequence(c("05:01:01:01", "06:01:01"), locus="DQB1")
hlaConvSequence(c("05:01", "06:01"), locus="DQB1", code="P.code")
hlaConvSequence(c("05:01", "06:01"), locus="DQB1", code="P.code.merge")



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")

(v <- hlaConvSequence(hla, code="P.code.merge"))
summary(v)

v <- hlaConvSequence(hla, code="P.code.merge", region="all")
summary(v)



hla.id <- "DQB1"
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")

(v <- hlaConvSequence(hla, code="P.code.merge"))
summary(v)

v <- hlaConvSequence(hla, code="P.code.merge", region="all")
summary(v)