atlasMaker: Identify the Gene-Feature Boundaries in HLA Region Genes
In HLAtools: Toolkit for HLA Immunogenomics
atlasMaker R Documentation
Identify the Gene-Feature Boundaries in HLA Region Genes
Description
The 'AA' atlas identifies the amino acid (AA) positions encoded by codons that span each exon (E) boundary. The 'cDNA' atlas describes the 3' nucleotide position in the cDNA sequence that follows each exon boundary, as well as the codon that spans each exon boundary. The 'gDNA' atlas describes first 3' nucleotide position following each UTR (U), exon or intron (I) boundary. Each feature is followed by its rank (e.g U3 is the 3' UTR). Non-standard gene-features (H, J, N, and S) are detailed in the documentation for the ffN() function.
Usage
atlasMaker(loci, source, version = "Latest")
Arguments
loci
A character string identifying a specific HLA gene (ex. "DRB1"). More than one gene can be specified (e.g., c("DRB1","DQB1")).
source
A character string identifying the type of alignment used to build the atlas. The allowed options are "AA", for protein alignments, "cDNA", for nucleotide alignments, and "gDNA", for genomic alignments. More than one alignment type can be specified (e.g., c("AA","gDNA")).
version
A character string identifying the release version of the IPD-IMGT/HLA Github repository for which alignments should be generated.
Details
Builds an 'atlas' of the gene-feature (exon, intron and UTR) boundaries for IPD-IMGT/HLA loci, using IPD-IMGT/HLA Database alignments.
Value
A list object of 'atlas' dataframes and a 'release version' character string for each locus and alignment type.
Note
For internal HLAtools use.
Nucleotide atlases for pseudogenes will include a 'codon' row populated with NA values.
Some HLA-DQB1\*05 and \*06 alleles include a 5th exon that is not present in the DQB1\*05:01:01:01 reference allele. In this case, the Exon 4 to Exon 5 boundary is defined as 'Ins' (insertion). For all other alleles there is no E.4-5 boundary.
Boundaries for non-standard hybrid (H), join (J), novel (N) and segment (S) features may be included in gene fragment and pseudogene atlases.
HLAtools documentation built on June 8, 2025, 12:24 p.m.
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| atlasMaker | R Documentation |
Identify the Gene-Feature Boundaries in HLA Region Genes
Description
The 'AA' atlas identifies the amino acid (AA) positions encoded by codons that span each exon (E) boundary. The 'cDNA' atlas describes the 3' nucleotide position in the cDNA sequence that follows each exon boundary, as well as the codon that spans each exon boundary. The 'gDNA' atlas describes first 3' nucleotide position following each UTR (U), exon or intron (I) boundary. Each feature is followed by its rank (e.g U3 is the 3' UTR). Non-standard gene-features (H, J, N, and S) are detailed in the documentation for the ffN() function.
Usage
atlasMaker(loci, source, version = "Latest")
Arguments
loci |
A character string identifying a specific HLA gene (ex. "DRB1"). More than one gene can be specified (e.g., c("DRB1","DQB1")). |
source |
A character string identifying the type of alignment used to build the atlas. The allowed options are "AA", for protein alignments, "cDNA", for nucleotide alignments, and "gDNA", for genomic alignments. More than one alignment type can be specified (e.g., c("AA","gDNA")). |
version |
A character string identifying the release version of the IPD-IMGT/HLA Github repository for which alignments should be generated. |
Details
Builds an 'atlas' of the gene-feature (exon, intron and UTR) boundaries for IPD-IMGT/HLA loci, using IPD-IMGT/HLA Database alignments.
Value
A list object of 'atlas' dataframes and a 'release version' character string for each locus and alignment type.
Note
For internal HLAtools use.
Nucleotide atlases for pseudogenes will include a 'codon' row populated with NA values.
Some HLA-DQB1\*05 and \*06 alleles include a 5th exon that is not present in the DQB1\*05:01:01:01 reference allele. In this case, the Exon 4 to Exon 5 boundary is defined as 'Ins' (insertion). For all other alleles there is no E.4-5 boundary.
Boundaries for non-standard hybrid (H), join (J), novel (N) and segment (S) features may be included in gene fragment and pseudogene atlases.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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