Gene Set Collection Indexes from the GeneSetDB Database
It prepares the GeneSetDB gene set collections to be used for the EGSEA analysis.
buildGeneSetDBIdx(entrezIDs, species, geneSets = "all", min.size = 1)
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.
character, determine the organism of selected gene sets: "human", "mouse" or "rat".
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.
integer, the minium number of genes required in a testing gene set
It indexes the GeneSetDB gene sets and loads gene set annotation.
indexed gene set annotation that can be used with other functions in
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
label a unique id that identifies the collection of gene
featureIDs stores the entrezIDs used in building the annotation,
stores that organism name of gene sets and
name stores the
to be used in the EGSEA report.
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