hlaConvSequence: Conversion From HLA Alleles to Amino Acid Sequences

In zhengxwen/HIBAG: HLA Genotype Imputation with Attribute Bagging

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, e.g., c("09:02"="107:01"), any "09:02" will be replaced by "107:01". Due to the change of HLA nomenclature from 2010, HLA-DPB1*09:02 is replaced by DPB1*107:01

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.

Value

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

Author(s)

Xiuwen Zheng

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")

# exact match
hlaConvSequence(c("01:01", "02:02", "01:01:01G", "01:01:01:01", "07"),
    locus="A")

# allow ambiguity
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)

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