## ----include=FALSE------------------------------------------------------------ library(knitr) opts_chunk$set(collapse = TRUE) ## ----------------------------------------------------------------------------- library(gep2pep) suppressMessages(library(GSEABase)) ## ----------------------------------------------------------------------------- ## db <- importMSigDB.xml("msigdb_v6.1.xml") ## db <- as.CategorizedCollection(db) ## ----------------------------------------------------------------------------- db <- loadSamplePWS() ## ----------------------------------------------------------------------------- colltypes <- sapply(db, collectionType) cats <- sapply(colltypes, attr, "category") subcats <- sapply(colltypes, attr, "subCategory") print(cats) print(subcats) makeCollectionIDs(db) ## ----collapse=TRUE------------------------------------------------------------ repoRoot <- file.path(tempdir(), "gep2pep_data") rp <- createRepository(repoRoot, db) ## ----------------------------------------------------------------------------- rp TFTsets <- loadCollection(rp, "c3_TFT") TFTsets description(TFTsets[["E47_01"]]) ## ----------------------------------------------------------------------------- geps <- loadSampleGEP() dim(geps) geps[1:5, 1:3] ## ----collapse=TRUE------------------------------------------------------------ buildPEPs(rp, geps) ## ----------------------------------------------------------------------------- loadESmatrix(rp, "c3_TFT")[1:3, 1:3] loadPVmatrix(rp, "c3_TFT")[1:3, 1:3] ## ----collapse=TRUE------------------------------------------------------------ pgset <- c("(+)_chelidonine", "(+/_)_catechin") psea <- CondSEA(rp, pgset) ## ----------------------------------------------------------------------------- getResults(psea, "c3_TFT") ## ----------------------------------------------------------------------------- sets <- loadCollection(rp, "c3_MIR") wM5012 <- which(sapply(sets, setIdentifier)=="M5012") wM18759 <- which(sapply(sets, setIdentifier)=="M18759") description(sets[[wM5012]]) description(sets[[wM18759]]) ## ----eval=FALSE--------------------------------------------------------------- # exportSEA(rp, psea) ## ----collapse=TRUE------------------------------------------------------------ pathways <- c("M11607", "M10817", "M16694", ## from c3_TFT "M19723", "M5038", "M13419", "M1094") ## from c4_CGN w <- sapply(db, setIdentifier) %in% pathways subdb <- db[w] psea <- PathSEA(rp, subdb) ## ----------------------------------------------------------------------------- getResults(psea, "c3_TFT") ## ----------------------------------------------------------------------------- pathways <- gene2pathways(rp, "FAM126A") pathways ## ----eval=F------------------------------------------------------------------- # download.file("http://dsea.tigem.it/data/Cmap_MSigDB_v6.1_PEPs.tar.gz", # "Cmap_MSigDB_v6.1_PEPs.tar.gz") # # untar("Cmap_MSigDB_v6.1_PEPs.tar.gz") # # rpBig <- openRepository("Cmap_MSigDB_v6.1_PEPs") ## ----eval=F------------------------------------------------------------------- # csea <- CondSEA(rpBig, c("scriptaid", "trichostatin_a", "valproic_acid", # "vorinostat", "hc_toxin", "bufexamac"), # collections=c("C5_BP", "C5_MF", "C5_CC")) # ## [16:41:40] Working on collection: C5_BP # ## [16:41:42] Common conditions removed from bgset # ## [16:41:42] Row-ranking collection # ## [16:41:48] Computing enrichments # ## [16:41:58] done # ## [16:41:58] Working on collection: C5_MF # ## [16:41:58] Row-ranking collection # ## [16:42:00] Computing enrichments # ## [16:42:02] done # ## [16:42:02] Working on collection: C5_CC # ## [16:42:02] Row-ranking collection # ## [16:42:03] Computing enrichments # ## [16:42:04] done ## ----eval=F------------------------------------------------------------------- # library(GSEABase) # setids <- sapply(loadCollection(rpBig, "C5_MF"), setIdentifier) # MFresults <- getResults(csea, "C5_MF") # w <- match(rownames(MFresults)[1:10], setids) # top10 <- loadCollection(rpBig, "C5_MF")[w] # sapply(top10, setName) # ## [1] "GO_TRANSCRIPTION_FACTOR_ACTIVITY_PROTEIN_BINDING" # ## [2] "GO_TRANSCRIPTION_COACTIVATOR_ACTIVITY" # ## [3] "GO_PHOSPHATIDYLCHOLINE_1_ACYLHYDROLASE_ACTIVITY" # ## [4] "GO_RETINOIC_ACID_RECEPTOR_BINDING" # ## [5] "GO_PRE_MRNA_BINDING" # ## [6] "GO_N_ACETYLTRANSFERASE_ACTIVITY" # ## [7] "GO_CYTOSKELETAL_PROTEIN_BINDING" # ## [8] "GO_PEPTIDE_N_ACETYLTRANSFERASE_ACTIVITY" # ## [9] "GO_ACETYLTRANSFERASE_ACTIVITY" # ## [10] "GO_HYDROGEN_EXPORTING_ATPASE_ACTIVITY" ## ----eval=F------------------------------------------------------------------- # exportSEA(rpBig, csea) ## ----eval=F------------------------------------------------------------------- # pws <- gene2pathways(rpBig, "TFEB") ## ----eval=F------------------------------------------------------------------- # psea <- PathSEA(rpBig, pws, collections=c("C5_BP", "C5_MF", "C5_CC")) # ## Warning: [17:17:13] There is at least one selected collections for # ## which no pathway has been provided # ## [17:17:13] Removing pathways not in specified collections # ## [17:17:13] Working on collection: C5_BP # ## [17:17:13] Common pathway sets removed from bgset # ## [17:17:15] Column-ranking collection # ## [17:17:22] Computing enrichments # ## [17:17:29] done # ## [17:17:29] Working on collection: C5_MF # ## [17:17:29] Common pathway sets removed from bgset # ## [17:17:29] Column-ranking collection # ## [17:17:30] Computing enrichments # ## [17:17:32] done ## ----eval=F------------------------------------------------------------------- # getResults(psea, "C5_BP")[1:10,] # ## ES PV # ## loperamide 0.7324720 1.504075e-11 # ## proadifen 0.7278256 2.079448e-11 # ## hydroquinine 0.7220082 3.110434e-11 # ## bepridil 0.6904276 2.616027e-10 # ## clomipramine 0.6891810 2.839879e-10 # ## alexidine 0.6741085 7.574142e-10 # ## digitoxigenin 0.6737685 7.741670e-10 # ## lanatoside_c 0.6651556 1.342553e-09 # ## helveticoside 0.6642112 1.425479e-09 # ## ouabain 0.6631157 1.527949e-09 ## ----eval=F------------------------------------------------------------------- # exportSEA(rpBig, psea) ## ----------------------------------------------------------------------------- rp$info("gep2pep repository") ## ----------------------------------------------------------------------------- rp ## ----------------------------------------------------------------------------- rp$info() ## ----collapse=TRUE------------------------------------------------------------ checkRepository(rp) ## ----include=FALSE------------------------------------------------------------ unlink(repoRoot, TRUE)