For retrieving the PIN file for an organism of your choice, you may
use the function get_pin_file()
. As of this version, the
only source for PIN data is “BioGRID”.
By default, the function downloads the PIN data from BioGRID and processes it, saves it in a temporary file and returns the path:
You can retrieve the PIN data for the organism of your choice, by
setting the org
argument:
You may also supply a path/to/PIN/file
to save the PIN
file for later use (in this case, the path you supply will be
returned):
## saving the "Homo_sapiens" PIN as "/path/to/PIN/file"
path_to_pin_file <- get_pin_file(path2pin = "/path/to/PIN/file")
You may also retrieve a specific version of BioGRID via setting the
release
argument:
To retrieve organism-specific gene sets list, you may use the
function get_gene_sets_list()
. The available sources for
gene sets are “KEGG”, “Reactome” and “MSigDB”. The function retrieves
the gene sets data from the source and processes it into a list of two
objects used by pathfindR for active-subnetwork-oriented enrichment
analysis: 1. gene_sets A list containing the genes
involved in each gene set 2. descriptions A named
vector containing the descriptions for each gene set
By default, get_gene_sets_list()
obtains “KEGG” gene
sets for “hsa”.
To obtain the gene sets list of the KEGG pathways for an organism of your choice, use the KEGG organism code for the selected organism. For a full list of all available organisms, see here.
For obtaining Reactome pathway gene sets, set the source
argument to “Reactome”. This downloads the most current Reactome
pathways in gmt format and processes it into the list object that
pathfindR uses:
For Reactome, there is only one collection of pathway gene sets.
Using msigdbr
, pathfindR
can retrieve all
MSigDB gene sets. For this, set the source
argument to
“MSigDB” and the collection
argument to the desired MSigDB
collection (one of H, C1, C2, C3, C4, C5, C6, C7):
The default organism for MSigDB is “Homo sapiens”, you may obtain the
gene sets data for another organism by setting the species
argument:
## obtaining C5 gene sets data for "Drosophila melanogaster"
gsets_list <- get_gene_sets_list(
source = "MSigDB",
species = "Drosophila melanogaster",
collection = "C5"
)
## see msigdbr::msigdbr_show_species() for all available organisms
msigdbr::msigdbr_show_species()
#> Warning in msigdbr::msigdbr_show_species(): 'msigdbr::msigdbr_show_species' is deprecated.
#> Use 'msigdbr_species' instead.
#> See help("Deprecated")
#> [1] "Anolis carolinensis" "Bos taurus"
#> [3] "Caenorhabditis elegans" "Canis lupus familiaris"
#> [5] "Danio rerio" "Drosophila melanogaster"
#> [7] "Equus caballus" "Felis catus"
#> [9] "Gallus gallus" "Homo sapiens"
#> [11] "Macaca mulatta" "Monodelphis domestica"
#> [13] "Mus musculus" "Ornithorhynchus anatinus"
#> [15] "Pan troglodytes" "Rattus norvegicus"
#> [17] "Saccharomyces cerevisiae" "Schizosaccharomyces pombe 972h-"
#> [19] "Sus scrofa" "Xenopus tropicalis"
You may also obtain the gene sets for a subcollection by setting the
subcollection
argument: