This data is prepared based on the molecular signatures database (Msigdb; http://www.broadinstitute.org/gsea/msigdb/index.jsp). An R object that contains associations between Msigdb C2:CPall (all pathways) gene sets and Human Entrez Genes. C2:CP gene sets are from the pathway databases, and usually are canonical representations of a biological process compiled by domain experts.
org.Hs.egMsigdbC2CPall <- dRDataLoader(RData.customised = "org.Hs.egMsigdbC2CPall")
an object of class "GS", a list with following components:
set_info: a matrix of nSet X 4 containing gene set information, where nSet is the number of gene sets, and the 4 columns are "setID" (i.e. "Geneset standard name"), "name" (i.e. "Geneset brief description"), "namespace" (i.e. Geneset category code) and "distance" (i.e. "Geneset full description")
gs: a list of gene sets, each storing gene members thereof. Always, gene sets are identified by "setID" and gene members identified by "Entrez ID"
Subramanian et al. (2005) Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci U S A., 102(43):15545-50.
org.Hs.egMsigdbC2CPall <- dRDataLoader(RData.customised='org.Hs.egMsigdbC2CPall')Error in dRDataLoader(RData.customised = "org.Hs.egMsigdbC2CPall"): unused argument (RData.customised = "org.Hs.egMsigdbC2CPall")names(org.Hs.egMsigdbC2CPall)Error in eval(expr, envir, enclos): object 'org.Hs.egMsigdbC2CPall' not found