getGeneSets | R Documentation |
This function retrieves gene sets for a given organism.
getGeneSets(
database = c("KEGG", "GO"),
org = "hsa",
taxid = 9606,
namespace = c("biological_process", "molecular_function", "cellular_component"),
minSize = 1,
maxSize = 1000,
useCache = FALSE
)
database |
The database of the gene sets. E.g, KEGG, GO. |
org |
The organism abbreviation. E.g, hsa, mmu, dme, etc. To see the full list of supported organisms, visit https://www.genome.jp/kegg/catalog/org_list.html. This parameter is only used when database is KEGG. |
taxid |
The NCBI taxonomy ID of the organism. This parameter is only used when database is GO. |
namespace |
The namespace of the GO terms. E.g, biological_process, molecular_function, cellular_component. |
minSize |
The minimum size of the gene sets. |
maxSize |
The maximum size of the gene sets. |
useCache |
A boolean parameter specifying if using pre-saved downloaded geneset database. It is FALSE by default. |
A named list with three elements: database, genesets and names.
library(RCPA)
KEGGgenesets <- getGeneSets("KEGG", org = "hsa",
minSize = 10, maxSize = 1000, useCache = TRUE)
GOterms <- getGeneSets("GO", taxid = 9606,
namespace = "biological_process",
minSize = 10, maxSize = 1000, useCache = TRUE)
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.