Gene Set Collection Indexes from the GeneSetDB Database

Description

It prepares the GeneSetDB gene set collections to be used for the EGSEA analysis.

Usage

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buildGeneSetDBIdx(entrezIDs, species, geneSets = "all", min.size = 1)

Arguments

entrezIDs

character, a vector that stores the Entrez Gene IDs tagged in your dataset. The order of the Entrez Gene IDs should match those of the count/expression matrix row names.

species

character, determine the organism of selected gene sets: "human", "mouse" or "rat".

geneSets

character, a vector determines which gene set collections are loaded from the GeneSetDB. It takes "all", "gsdbdis", "gsdbgo", "gsdbdrug", "gsdbpath" or "gsdbreg". "all" includes all the GeneSetDB collections. "gsdbdis" is to load the disease collection, "gsdbgo" to load the GO terms collection, "gsdbdrug" to load the drug/chemical collection, "gsdbpath" to load the pathways collection and "gsdbreg" to load the gene regulation collection.

min.size

integer, the minium number of genes required in a testing gene set

Details

It indexes the GeneSetDB gene sets and loads gene set annotation.

Value

indexed gene set annotation that can be used with other functions in the package. Each annotation is a list of seven elements: original stores the original gene sets, idx stores the indexed gene sets, anno that stores detailed annotation for each gene set, label a unique id that identifies the collection of gene sets, featureIDs stores the entrezIDs used in building the annotation, species stores that organism name of gene sets and name stores the collection name to be used in the EGSEA report.

Examples

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library(EGSEAdata)
data(il13.data)
v = il13.data$voom
gs.annots = buildGeneSetDBIdx(entrezIDs=rownames(v$E), species="human")
names(gs.annots)