Gene synonyms

Source: R/geneSynonyms.R

Look up gene synonyms from NCBI.

geneSynonyms(
  organism,
  taxonomicGroup = NULL,
  geneIdType = c("Entrez", "Ensembl", "HGNC", "OMIM")
)

Arguments

organism

character(1). Full Latin organism name (e.g. "Homo sapiens").
taxonomicGroup

character(1). NCBI FTP server taxonomic group subdirectory path (e.g. "Mammalia"). Defining this manually avoids having to query the FTP server.
geneIdType

character(1). Type of gene identifier to return in the geneId column.

Value

DataFrame containing geneId and geneSynonyms columns.

Note

Updated 2021-02-13.

Caenorhabditis elegans

Synonym support for Caenorhabditis elegans is poor on NCBI. Use the WormBase package instead.

Examples

object <- geneSynonyms(
    organism = "Homo sapiens",
    taxonomicGroup = "Mammalia",
    geneIdType = "Ensembl"
)

#> → Downloading Homo sapiens gene info from NCBI at <ftp://ftp.ncbi.nih.gov/gene/DATA/GENE_INFO/Mammalia/Homo_sapiens.gene_info.gz>.
#> → Importing af13430a6cd5_Homo_sapiens.gene_info.gz at /opt/koopa/opt/r/cache/AcidGenomes using data.table::`fread()`.
print(object)

#> DataFrame with 22767 rows and 2 columns
#>                          geneId             geneSynonyms
#>                     <character>          <CharacterList>
#> ENSG00000000003 ENSG00000000003      T245,TM4SF6,TSPAN-6
#> ENSG00000000005 ENSG00000000005         BRICD4,CHM1L,TEM
#> ENSG00000000419 ENSG00000000419               CDGIE,MPDS
#> ENSG00000000457 ENSG00000000457             PACE-1,PACE1
#> ENSG00000000938 ENSG00000000938 c-fgr,c-src2,p55-Fgr,...
#> ...                         ...                      ...
#> ENSG00000288616 ENSG00000288616  ELOA3D,ELOA3L2,TCEB3CL2
#> ENSG00000288638 ENSG00000288638                   YYLNCT
#> ENSG00000288642 ENSG00000288642         CDR,CDR34,CDR62A
#> ENSG00000288649 ENSG00000288649       C20orf134,dJ63M2.2
#> ENSG00000288675 ENSG00000288675                     PANO