Gene Set Collection Indexes from the MSigDB Database
It prepares the MSigDB gene set collections to be used for the EGSEA analysis.
buildMSigDBIdx(entrezIDs, geneSets = "all", species = "Homo sapiens", 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, a vector determines which gene set collections should be used from the MSigDB. It can take values from this list: "all", "h", "c1", "c2", "c3", "c4", "c5", "c6","c7". "c1" is human specific. If "all", all available gene set collections are loaded.
character, determine the organism of selected gene sets: "human", "mouse" or "rat".
integer, the minium number of genes required in a testing gene set
It indexes the MSigDB 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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