buildMSigDBIdx: Gene Set Collection Indexes from the MSigDB Database

Description Usage Arguments Details Value Examples

Description

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

Usage

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buildMSigDBIdx(entrezIDs, species = "Homo sapiens", geneSets = "all",
  go.part = FALSE, 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 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.

go.part

logical, whether to partition the C5 collection into the three GO domains: CC, MF and BP or use the entire collection all together.

min.size

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

Details

It indexes the MSigDB 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$voom
gs.annots = buildMSigDBIdx(entrezIDs=rownames(v$E), species="human",
geneSets=c("h", "c2"))
names(gs.annots)


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