### R code from vignette source 'splineTimeR.Rnw' ################################################### ### code chunk number 1: splineTimeR.Rnw:62-66 (eval = FALSE) ################################################### ## #path1 <- "/Users/hbraselmann/R/Bioc3.4dev/library" ## #path2 <- "/Library/Frameworks/R.framework/Versions/3.3/Resources/library" ## #.libPaths(c(path1, path2)) ## #.libPaths() ################################################### ### code chunk number 2: splineTimeR.Rnw:69-72 ################################################### library(splineTimeR) data(TCsimData) head(pData(TCsimData),8) ################################################### ### code chunk number 3: splineTimeR.Rnw:100-104 ################################################### diffExprs <- splineDiffExprs(eSetObject = TCsimData, df = 3, cutoff.adj.pVal = 0.01, reference = "T1", intercept = TRUE) head(diffExprs, 3) ################################################### ### code chunk number 4: splineTimeR.Rnw:112-114 ################################################### splinePlot(eSetObject = TCsimData, df = 3, reference = "T1", toPlot = c("EEF2","OR5W2")) ################################################### ### code chunk number 5: splineTimeR.Rnw:138-155 (eval = FALSE) ################################################### ## ## Not run ## ## Download .gmt file 'c2.all.v5.0.symbols.gmt' (all curated gene sets, ## ## gene symbols) from the Broad, ## ## http://www.broad.mit.edu/gsea/downloads.jsp#msigdb, then ## geneSets <- getGmt("/path/to/c2.all.v5.0.symbols.gmt") ## ## ## load ExpressionSet object containing simulated time-course data ## data(TCsimData) ## ## ## check for differentially expressed genes ## diffExprs <- splineDiffExprs(eSetObject = TCsimData, df = 3, ## cutoff.adj.pVal = 0.01, reference = "T1") ## ## ## use differentially expressed genes for pathway enrichment analysis ## enrichPath <- pathEnrich(geneList = rownames(diffExprs), geneSets = geneSets, ## universe = 6536) ## ## End(Not run) ################################################### ### code chunk number 6: splineTimeR.Rnw:160-171 (eval = FALSE) ################################################### ## ## Not run ## ## Download and unzip .gmt.zip file 'ReactomePathways.gmt.zip' ## ## ("Reactome Pathways Gene Set" under "Specialized data formats") from ## ## the Reactome website http://www.reactome.org/pages/download-data/, then ## geneSets <- getGmt("/path/to/ReactomePathways.gmt") ## data(TCsimData) ## diffExprs <- splineDiffExprs(eSetObject = TCsimData, df = 3, ## cutoff.adj.pVal = 0.01, reference = "T1") ## enrichPath <- pathEnrich(geneList = rownames(diffExprs), geneSets = geneSets, ## universe = 6536) ## ## End(Not run) ################################################### ### code chunk number 7: single_igr ################################################### igr <- splineNetRecon(eSetObject = TCsimData, treatmentType = "T2", probesForNR = rownames(diffExprs), cutoff.ggm = 0.7, method = "dynamic") ################################################### ### code chunk number 8: plot_igr1 ################################################### plot(igr, vertex.label = NA, vertex.size = 3, main = "igraph_0.7") ################################################### ### code chunk number 9: two_igraphs ################################################### igr <- splineNetRecon(eSetObject = TCsimData, treatmentType = "T2", probesForNR = rownames(diffExprs), cutoff.ggm = c(0.8,0.9), method = "dynamic") ################################################### ### code chunk number 10: plot_igrlist ################################################### plot(igr[[1]], vertex.label = NA, vertex.size = 3, main = "igraph_0.8") plot(igr[[2]], vertex.label = NA, vertex.size = 3, main = "igraph_0.9") ################################################### ### code chunk number 11: splineTimeR.Rnw:233-238 (eval = FALSE) ################################################### ## library(FIs) ## data(FIs) ## names(FIs) ## head(FIs$FIs_Reactome) ## head(FIs$FIs_BioGRID) ################################################### ### code chunk number 12: splineTimeR.Rnw:243-248 ################################################### igr <- splineNetRecon(eSetObject = TCsimData, treatmentType = "T2", probesForNR = rownames(diffExprs), cutoff.ggm = c(0.7,0.8,0.9), method = "dynamic") scaleFreeProp <- networkProperties(igr) head(scaleFreeProp)