Get pathways/GOslim collections from PANTHER.db Biocondcutor package.

Source: R/get-panther.R

This is a convience function that orchestrates the PANTHER.db package to return GeneSetDb objects for either pathway or GOslim information for human or mouse.

getPantherCollection(
  type = c("pathway", "goslim"),
  species = c("human", "mouse")
)

getPantherGeneSetDb(
  type = c("pathway", "goslim"),
  species = c("human", "mouse")
)

Arguments

type

"pathway" or, "goslim"

species

"human" or "mouse"

Value

A BiocSet of panther pathways

Details

Note that for some reason the PANTHER.db package needs to be installed in a user-writable package location for this to work properly. If you see an error like "Error in resqlite_send_query ... attempt to write a readonly database", this is the problem. Please install another version of the PANTHER.db package in a user-writable directory using BiocManager::install().

Functions

  • getPantherGeneSetDb(): returns a GeneSetDb

GOSLIM

GO Slims are "cut down" versions of the GO ontology that contain a subset of the terms in the whole GO.

PANTHER provides their own set of GO slims, although it's not clear how often these get updated.

Examples

# \donttest{
# this requires you have the PANTHER.db package installed via BiocManager
bsc.panther <- getPantherCollection(species = "human")
#> Error in getPantherGeneSetDb(type, species): org.Hs.eg.db bioconductor package required for this species query
#> 
#> Warning: download failed
#>   web resource path: ‘https://annotationhub.bioconductor.org/fetch/120820’
#>   local file path: ‘/github/home/.cache/R/AnnotationHub/1d6754deb882_120820’
#>   reason: Failed to perform HTTP request.
#> Caused by error in `curl::curl_fetch_disk()`:
#> ! Timeout was reached [mghp.osn.xsede.org]:
#> SSL connection timeout
#> Warning: bfcadd() failed; resource removed
#>   rid: BFC3
#>   fpath: ‘https://annotationhub.bioconductor.org/fetch/120820’
#>   reason: download failed
#> Warning: download failed
#>   hub path: ‘https://annotationhub.bioconductor.org/fetch/120820’
#>   cache resource: ‘AH114074 : 120820’
#>   reason: bfcadd() failed; see warnings()
#> Error loading resource.
#>  attempting to re-download
#> Warning: download failed
#>   web resource path: ‘https://annotationhub.bioconductor.org/fetch/120820’
#>   local file path: ‘/github/home/.cache/R/AnnotationHub/1d67a0c5589_120820’
#>   reason: Failed to perform HTTP request.
#> Caused by error in `curl::curl_fetch_disk()`:
#> ! Timeout was reached [mghp.osn.xsede.org]:
#> SSL connection timeout
#> Warning: bfcadd() failed; resource removed
#>   rid: BFC4
#>   fpath: ‘https://annotationhub.bioconductor.org/fetch/120820’
#>   reason: download failed
#> Warning: download failed
#>   hub path: ‘https://annotationhub.bioconductor.org/fetch/120820’
#>   cache resource: ‘AH114074 : 120820’
#>   reason: bfcadd() failed; see warnings()
#> Warning: .onUnload failed in unloadNamespace() for 'PANTHER.db', details:
#>   call: NULL
#>   error: failed to load resource
#>   name: AH114074
#>   title: PANTHER.db database
#>   reason: 1 resources failed to download
# }