Map gene names to NCBI

Map gene names to NCBI

Usage

mapGeneNamesToNcbi(genes, organism, taxonomicGroup = NULL, ncbi = NULL)

Arguments

genes

character. Gene names (e.g. "TUT4").

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.

ncbi

NcbiGeneIfo or NULL. If NULL, NCBI annotations will be downloaded automatically.

Note

Updated 2023-03-03.

Examples

## Homo sapiens.
x <- mapGeneNamesToNcbi(
    genes = c("TUT4", "ZCCHC11", "TENT3A"),
    organism = "Homo sapiens"
)
#> → Downloading Homo sapiens gene info from NCBI at <https://ftp.ncbi.nih.gov/gene/DATA/GENE_INFO/Mammalia/Homo_sapiens.gene_info.gz>.
#> → Importing /Users/mike/.cache/R/AcidGenomes/BiocFileCache/89e51cc73760_Homo_sapiens.gene_info.gz using base::`read.table()`.
print(x)
#> [1] 23318 23318 23318

## Mus musculus.
x <- mapGeneNamesToNcbi(
    genes = c("Nfe2l2", "Nrf2"),
    organism = "Mus musculus"
)
#> → Downloading Mus musculus gene info from NCBI at <https://ftp.ncbi.nih.gov/gene/DATA/GENE_INFO/Mammalia/Mus_musculus.gene_info.gz>.
#> → Importing /Users/mike/.cache/R/AcidGenomes/BiocFileCache/8e9976c0388a_Mus_musculus.gene_info.gz using base::`read.table()`.
print(x)
#> [1] 18024 18024