Look up gene synonyms from NCBI.

geneSynonyms(organism)

Arguments

organism

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

Value

SplitDataFrameList. Split by geneID column. Handles genes with duplicate entries (e.g. ENSG00000004866).

Note

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

Updated 2019-08-18.

Examples

options(acid.test = TRUE) x <- geneSynonyms(organism = "Homo sapiens")
#> Decompressing 'homo_sapiens.gene_info.gz' in 'tempdir()'.
#> Importing 'homo_sapiens.gene_info.gz' using 'data.table::fread()'.
#> SplitDataFrameList of length 8 #> $ENSG00000114771 #> DataFrame with 1 row and 3 columns #> geneID geneName synonyms #> <character> <character> <character> #> 1 ENSG00000114771 AADAC CES5A1, DAC #> #> $ENSG00000121410 #> DataFrame with 1 row and 3 columns #> geneID geneName synonyms #> <character> <character> <character> #> 1 ENSG00000121410 A1BG A1B, ABG, GAB, HYST2477 #> #> $ENSG00000129673 #> DataFrame with 1 row and 3 columns #> geneID geneName synonyms #> <character> <character> <character> #> 1 ENSG00000129673 AANAT DSPS, SNAT #> #> $ENSG00000156006 #> DataFrame with 1 row and 3 columns #> geneID geneName synonyms #> <character> <character> <character> #> 1 ENSG00000156006 NAT2 AAC2, NAT-2, PNAT #> #> $ENSG00000171428 #> DataFrame with 1 row and 3 columns #> geneID geneName synonyms #> <character> <character> <character> #> 1 ENSG00000171428 NAT1 AAC1, MNAT, NAT-1, NATI #> #> $ENSG00000175899 #> DataFrame with 1 row and 3 columns #> geneID geneName synonyms #> <character> <character> <character> #> 1 ENSG00000175899 A2M A2MD, CPAMD5, FWP007, S863-7 #> #> $ENSG00000196136 #> DataFrame with 1 row and 3 columns #> geneID geneName synonyms #> <character> <character> <character> #> 1 ENSG00000196136 SERPINA3 AACT, ACT, GIG24, GIG25 #> #> $ENSG00000256069 #> DataFrame with 1 row and 3 columns #> geneID geneName synonyms #> <character> <character> <character> #> 1 ENSG00000256069 A2MP1 A2MP #>