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PANTHER database annotations

Source: R/AllGenerators.R
PANTHER.Rd

PANTHER gene ontology definitions. PANTHER stands for Protein ANalysis THrough Evolutionary Relationships.

Usage

PANTHER(organism, release = "18.0")

Arguments

organism

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

release

character(1) or NULL. PANTHER release version. If NULL, defaults to current release. Consult the PANTHER website for a list of release versions available from the FTP server (e.g. "17.0").

Value

PANTHER.

Note

Updated 2023-09-25.

Suported organisms

  • Caenorhabditis elegans

  • Drosophila melanogaster

  • Homo sapiens

  • Mus musculus

Examples

x <- PANTHER(organism = "Homo sapiens")
#> → Downloading PANTHER 18.0 annotations for Homo sapiens.
#> → Importing /Users/mike/.cache/R/PANTHER/BiocFileCache/3e3522ce32b8_PTHR18.0_human using base::`read.table()`.
#> → Importing HGNC complete set.
#> → Importing /Users/mike/.cache/R/AcidGenomes/BiocFileCache/354235173cdc_hgnc_complete_set.txt using base::`readLines()`.
#> → Importing text connection with base::`read.table()`.
#> ! 1 duplicated gene identifier detected: ENSG00000277758.
#> → Splitting and sorting the GO terms.
print(x)
#> PANTHER 0.5.0 with 19333 rows and 11 columns
#> organism: Homo sapiens
#> release: 18.0
#> genes(19333): ENSG00000000003 ENSG00000000005 ... ENSG00000290292 ENSG00000291237