geneSynonyms: Gene synonyms

Description Usage Arguments Value Caenorhabditis elegans Note Examples

View source: R/geneSynonyms.R

Description

Look up gene synonyms from NCBI.

Usage

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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.

Caenorhabditis elegans

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

Note

Updated 2021-02-13.

Examples

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

acidgenomics/AcidGenomes documentation built on Sept. 16, 2021, 7:30 p.m.