Load gene set data — loadGeneSet • WebGestaltR

Load gene set data

Usage

loadGeneSet(
  organism = "hsapiens",
  enrichDatabase = NULL,
  enrichDatabaseFile = NULL,
  enrichDatabaseType = NULL,
  enrichDatabaseDescriptionFile = NULL,
  cache = NULL,
  hostName = "https://www.webgestalt.org/",
  isMultiOmics = FALSE
)

Arguments

organism: Currently, WebGestaltR supports 12 organisms. Users can use the function listOrganism to check available organisms. Users can also input others to perform the enrichment analysis for other organisms not supported by WebGestaltR. For other organisms, users need to provide the functional categories, interesting list and reference list (for ORA method). Because WebGestaltR does not perform the ID mapping for the other organisms, the above data should have the same ID type.
enrichDatabase: The functional categories for the enrichment analysis. Users can use the function listGeneSet to check the available functional databases for the selected organism. Multiple databases in a vector are supported for ORA and GSEA.
enrichDatabaseFile: Users can provide one or more GMT files as the functional category for enrichment analysis. The extension of the file should be gmt and the first column of the file is the category ID, the second one is the external link for the category. Genes annotated to the category are from the third column. All columns are separated by tabs. The GMT files will be combined with enrichDatabase.
enrichDatabaseType: The ID type of the genes in the enrichDatabaseFile. If users set organism as others, users do not need to set this ID type because WebGestaltR will not perform ID mapping for other organisms. The supported ID types of WebGestaltR for the selected organism can be found by the function listIdType.
enrichDatabaseDescriptionFile: Users can also provide description files for the custom enrichDatabaseFile. The extension of the description file should be des. The description file contains two columns: the first column is the category ID that should be exactly the same as the category ID in the custom enrichDatabaseFile and the second column is the description of the category. All columns are separated by tabs.
cache: A directory to save data cache for reuse. Defaults to NULL and disabled.
hostName: The server URL for accessing data. Mostly for development purposes.
isMultiOmics: Boolean if loading gene sets for multiomics. Defaults to FALSE.

Value

A list of geneSet, geneSetDes, geneSetDag, geneSetNet, standardId.

geneSet: Gene set: A data frame with columns of "geneSet", "description", "genes"
geneSetDes: Description: A data frame with columns of two columns of gene set ID and description
geneSetDag: DAG: A edge list data frame of two columns of parent and child. Or a list of data frames if multilple databases are given.
geneSetNet: Network: A edge list data frame of two columns connecting nodes. Or a list of data frames if multilple databases are given.
standardId: The standard ID of the gene set