EGSEA (version 1.0.3)

buildIdxEZID: Generate Gene Set Collection Indexes from the MSigDB and KEGG Databases

Description

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

Usage

buildIdxEZID(entrezIDs, species = "human", msigdb.gsets = NULL, kegg.updated = FALSE, kegg.exclude = c(), min.size = 1, rdata.dir = NULL)

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".

msigdb.gsets

character, a vector determines which gene set collections should be used. It can take values from this list: "h", "c1", "c2", "c3", "c4", "c5", "c6","c7". "h" and "c1" are human specific. If NULL, all available gene set collections are loaded. If "none", MSigDB collections are excluded.

kegg.updated

logical, set to TRUE if you want to download the most recent KEGG pathways.

kegg.exclude

character, vector used to exclude KEGG pathways of specific type(s): Disease, Metabolism, Signaling. If "all", none fo the KEGG collections is included.

min.size

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

rdata.dir

character, directory from which the MSigDB collections are loaded. If NULL, EGSEA tries to load the data from EGSEAdata.

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.

Details

It indexes the MSigDB and KEGG gene sets and loads gene set annotation.

Examples

library(EGSEAdata)
data(il13.data)
v = il13.data$voom
gs.annots = buildIdxEZID(entrezIDs=rownames(v$E), species="human",
         msigdb.gsets = c("h", "c2"),
         kegg.exclude = c("Metabolism"))
names(gs.annots)