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Import NCBI (Entrez) gene identifier information

Source: R/NcbiGeneInfo.R
NcbiGeneInfo.Rd

Import NCBI (Entrez) gene identifier information

Usage

NcbiGeneInfo(organism, taxonomicGroup = NULL, refseqGeneSummary = FALSE)

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.

refseqGeneSummary

logical(1). Include RefSeq gene summary in "refseqGeneSummary" column. Requires Bioconductor GeneSummary package to be installed.

Value

NcbiGeneInfo.

Note

Updated 2023-12-19.

See also

  • https://ftp.ncbi.nlm.nih.gov/gene/DATA/GENE_INFO/

Examples

object <- NcbiGeneInfo(
    organism = "Homo sapiens",
    taxonomicGroup = "Mammalia"
)
#> → Downloading Homo sapiens gene info from NCBI at <https://ftp.ncbi.nlm.nih.gov/gene/DATA/GENE_INFO/Mammalia/Homo_sapiens.gene_info.gz>.
#> Error in h(simpleError(msg, call)): error in evaluating the argument 'con' in selecting a method for function 'import': formal argument "USE.NAMES" matched by multiple actual arguments
print(object)
#> Error: object 'object' not found