README.md

In datarail/genebabel: Convert Gene Symbols and Genes

genebabel

The genebabel package is designed to make it easy to convert gene identifiers and symbols between different databases.

Included at the moment are the HUGO Gene Nomenclature Consortium (HGNC) database of human genes. A convenient feature is that also alternative and previous symbols, which are no longer in use, are included and can be queried.

Installation

devtools::install_github("datarail/genebabel")

Example uses

Query the HGNC databse using a character vector of gene symbols. Some of them might be out of date, therefore also previous and alias symbols are queried.

library(genebabel)
query_hgnc(c("FLG", "SGK2"), c("symbol", "alias_symbol", "prev_symbol"))
#> # A tibble: 2 x 52
#>   query hgnc_id name  locus_group locus_type status location
#>   <chr> <chr>   <chr> <chr>       <chr>      <chr>  <chr>   
#> 1 FLG   HGNC:3… fila… protein-co… gene with… Appro… 1q21.3  
#> 2 SGK2  HGNC:1… SGK2… protein-co… gene with… Appro… 20q13.12
#> # ... with 45 more variables: location_sortable <chr>,
#> #   alias_symbol <list>, alias_name <list>, prev_symbol <list>,
#> #   prev_name <list>, gene_family <list>, gene_family_id <list>,
#> #   date_approved_reserved <chr>, date_symbol_changed <chr>,
#> #   date_name_changed <chr>, date_modified <chr>, entrez_id <chr>,
#> #   ensembl_gene_id <chr>, vega_id <chr>, ucsc_id <chr>, ena <list>,
#> #   refseq_accession <list>, ccds_id <list>, uniprot_ids <list>,
#> #   pubmed_id <list>, mgd_id <list>, rgd_id <list>, lsdb <list>,
#> #   cosmic <chr>, omim_id <list>, mirbase <chr>, homeodb <int>,
#> #   snornabase <chr>, bioparadigms_slc <chr>, orphanet <int>,
#> #   pseudogene.org <chr>, horde_id <chr>, merops <chr>, imgt <chr>,
#> #   iuphar <chr>, kznf_gene_catalog <int>, `mamit-trnadb` <int>, cd <chr>,
#> #   lncrnadb <chr>, enzyme_id <list>, intermediate_filament_db <chr>,
#> #   rna_central_ids <list>, lncipedia <chr>, symbol <chr>, match__ <chr>

Query the HGNC databse using a data frame. The b column contains gene symbols, some of which might be out of date, therefore also previous and alias symbols are queried.

library(genebabel)
d <- data.frame(a = 1:3, b = c("FLG", "SGK2", "CDK1"))
join_hgnc(d, "b",
  match_cols = c("symbol", "alias_symbol", "prev_symbol"),
  select_cols = c("entrez_id", "symbol", "refseq_accession"))
#>   a    b entrez_id symbol refseq_accession
#> 1 1  FLG      2312    FLG        NM_002016
#> 2 2 SGK2     10110   SGK2     NM_001199264
#> 3 3 CDK1       983   CDK1        NM_001786

datarail/genebabel documentation built on Sept. 20, 2019, 3:50 p.m.