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

PANTHER(organism, release = NULL,
  BPPARAM = BiocParallel::SerialParam(progressbar = TRUE))

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. "14.0").

BPPARAM

bpparamClass. BiocParallel parameter to specify the desired processor configuration.
We recommend using one of the following:

Value

PANTHER.

Note

Updated 2019-08-27.

Suported organisms

  • Caenorhabditis elegans

  • Drosophila melanogaster

  • Homo sapiens

  • Mus musculus

Examples

options(acid.test = TRUE) x <- PANTHER( organism = "Homo sapiens", BPPARAM = BiocParallel::SerialParam() )
#> Downloading PANTHER annotations for 'Homo sapiens' (current release).
#> Decompressing 'PTHR13.1_human.gz' in 'tempdir()'.
#> Importing 'PTHR13.1_human' using 'data.table::fread()'.
#> Importing HGNC to Ensembl gene ID mappings.
#> Decompressing 'hgnc.txt.gz' in 'tempdir()'.
#> Importing 'hgnc.txt' using 'data.table::fread()'.
#> Splitting and sorting the GO terms.
#> PANTHER 0.1.0 of length 9 #> organism: Homo sapiens #> release: current_release #> genes(10): ENSG00000010219 ENSG00000075188 ... ENSG00000197140 ENSG00000213886