## ----eval=TRUE, out.height.px=6, out.width.px=6------------------------------- suppressMessages(library(ADAM)) ## ----eval=TRUE, out.height.px=6, out.width.px=6------------------------------- data("ExpressionAedes") head(ExpressionAedes) ## ----eval=TRUE, out.height.px=6, out.width.px=6------------------------------- Comparison <- c("control1,experiment1","control2,experiment2") ## ----eval=TRUE, out.height.px=6, out.width.px=6------------------------------- Minimum <- 3 Maximum <- 20 ## ----eval=TRUE, out.height.px=6, out.width.px=6------------------------------- SeedBootstrap <- 1049 StepsBootstrap <- 1000 ## ----eval=TRUE, out.height.px=6, out.width.px=6------------------------------- CutoffValue <- 0.05 MethodCorrection <- "fdr" ## ----eval=TRUE, out.height.px=6, out.width.px=6------------------------------- data("KeggPathwaysAedes") head(KeggPathwaysAedes) ## ----eval=TRUE, out.height.px=6, out.width.px=6------------------------------- Domain <- "own" Nomenclature <- "geneStableID" ## ----eval=TRUE, out.height.px=6, out.width.px=6------------------------------- Wilcoxon <- TRUE Fisher <- TRUE ## ----eval=TRUE, out.height.px=6, out.width.px=6------------------------------- ResultAnalysis <- suppressMessages(GFAGAnalysis(ComparisonID = Comparison, ExpressionData = ExpressionAedes, MinGene = Minimum, MaxGene = Maximum, SeedNumber = SeedBootstrap, BootstrapNumber = StepsBootstrap, PCorrection = CutoffValue, DBSpecies = KeggPathwaysAedes, PCorrectionMethod = MethodCorrection, WilcoxonTest = Wilcoxon, FisherTest = Fisher, AnalysisDomain = Domain, GeneIdentifier = Nomenclature)) ## ----eval=TRUE, out.height.px=6, out.width.px=6------------------------------- head(ResultAnalysis[[1]]) ## ----eval=TRUE, out.height.px=6, out.width.px=6------------------------------- DT::datatable(as.data.frame(ResultAnalysis[[2]][1]), width = 800, options = list(scrollX = TRUE)) DT::datatable(as.data.frame(ResultAnalysis[[2]][2]), width = 800, options = list(scrollX = TRUE)) ## ----eval=TRUE, out.height.px=6, out.width.px=6------------------------------- suppressMessages(library(ADAM)) data("ExpressionAedes") data("KeggPathwaysAedes") ## ----eval=TRUE, out.height.px=6, out.width.px=6------------------------------- Comparison <- c("control1,experiment1") Minimum <- 3 Maximum <- 100 ## ----eval=TRUE, out.height.px=6, out.width.px=6------------------------------- SpeciesID <- "KeggPathwaysAedes" ## ----eval=TRUE, out.height.px=6, out.width.px=6------------------------------- Domain <- "own" Nomenclature <- "geneStableID" ## ----eval=TRUE, out.height.px=6, out.width.px=6------------------------------- ResultAnalysis <- suppressMessages(ADAnalysis(ComparisonID = Comparison, ExpressionData = ExpressionAedes, MinGene = Minimum, MaxGene = Maximum, DBSpecies = KeggPathwaysAedes, AnalysisDomain = Domain, GeneIdentifier = Nomenclature)) ## ----eval=TRUE, out.height.px=6, out.width.px=6------------------------------- head(ResultAnalysis[[1]]) ## ----eval=TRUE, out.height.px=6, out.width.px=6------------------------------- DT::datatable(as.data.frame(ResultAnalysis[[2]][1]), width = 800, options = list(scrollX = TRUE)) ## ----eval=TRUE, out.height.px=6, out.width.px=6, label='Session information', , echo=FALSE---- sessionInfo()