## ----message = FALSE---------------------------------------------------------- library(transcriptogramer) t <- transcriptogramPreprocess(association = association, ordering = Hs900) ## ----message = FALSE---------------------------------------------------------- ## during the preprocessing ## creating the object and setting the radius as 0 t <- transcriptogramPreprocess(association = association, ordering = Hs900) ## creating the object and setting the radius as 80 t <- transcriptogramPreprocess(association = association, ordering = Hs900, radius = 80) ## ----message = FALSE---------------------------------------------------------- ## after the preprocessing ## modifying the radius of an existing Transcriptogram object radius(object = t) <- 50 ## getting the radius of an existing Transcriptogram object r <- radius(object = t) ## ----message = FALSE, comment = ""-------------------------------------------- oPropertiesR50 <- orderingProperties(object = t, nCores = 1) ## slight change of radius radius(object = t) <- 80 ## this output is partially different comparing to oPropertiesR50 oPropertiesR80 <- orderingProperties(object = t, nCores = 1) sum(oPropertiesR50$windowModularity) sum(oPropertiesR80$windowModularity) ## ----message = FALSE---------------------------------------------------------- cProperties <- connectivityProperties(object = t) ## ----message = FALSE---------------------------------------------------------- t <- transcriptogramStep1(object = t, expression = GSE9988, dictionary = GPL570, nCores = 1) t2 <- t ## ----message = FALSE---------------------------------------------------------- t <- transcriptogramStep2(object = t, nCores = 1) ## ----message = FALSE---------------------------------------------------------- radius(object = t2) <- 50 t2 <- transcriptogramStep2(object = t2, nCores = 1) ## ----message = FALSE, fig.show = "hide"--------------------------------------- ## trend = FALSE for microarray data or voom log2-counts-per-million ## the default value for trend is FALSE levels <- c(rep(FALSE, 3), rep(TRUE, 3)) t <- differentiallyExpressed(object = t, levels = levels, pValue = 0.01, trend = FALSE, title = "radius 80") ## the radius 50 will affect the output significantly t2 <- differentiallyExpressed(object = t2, levels = levels, pValue = 0.01, species = DEsymbols, title = "radius 50") ## ----eval = FALSE------------------------------------------------------------- # ## using the species argument to translate ENSEMBL Peptide IDs to Symbols # ## Internet connection is required for this command # t <- differentiallyExpressed(object = t, levels = levels, pValue = 0.01, # species = "Homo sapiens", title = "radius 80") # # ## translating ENSEMBL Peptide IDs to Symbols using the DEsymbols dataset # t <- differentiallyExpressed(object = t, levels = levels, pValue = 0.01, # species = DEsymbols, title = "radius 80") ## ----message = FALSE, comment = ""-------------------------------------------- DE <- DE(object = t) DE2 <- DE(object = t2) nrow(DE) nrow(DE)/length(unique(DE$ClusterNumber)) nrow(DE2) nrow(DE2)/length(unique(DE2$ClusterNumber)) ## ----eval = FALSE------------------------------------------------------------- # rdp <- clusterVisualization(object = t) ## ----message = FALSE---------------------------------------------------------- ## using the HsBPTerms dataset to create the Protein2GO data.frame t <- clusterEnrichment(object = t, species = HsBPTerms, pValue = 0.005, nCores = 1) ## ----eval = FALSE------------------------------------------------------------- # ## using the species argument to create the Protein2GO data.frame # ## Internet connection is required for this command # t <- clusterEnrichment(object = t, species = "Homo sapiens", # pValue = 0.005, nCores = 1) ## ----eval = FALSE------------------------------------------------------------- # head(Terms(t)) ## ----echo = FALSE, comment = ""----------------------------------------------- load("terms.RData") head(terms) ## ----eval = FALSE------------------------------------------------------------- # enrichmentPlot(t) ## ----------------------------------------------------------------------------- sessionInfo() ## ----------------------------------------------------------------------------- warnings()