groupedGSEAtoStackedReport {NanoTube} | R Documentation |
After clustering FGSEA results by gene set similarity, this function builds a report containing the individual gene expression profiles for genes contained in each gene set cluster.
groupedGSEAtoStackedReport(grouped.gsea, leadingEdge, de.fit, outputDir = NULL)
grouped.gsea |
Output from groupFGSEA() |
leadingEdge |
Leading edge analysis results used in groupFGSEA() |
de.fit |
Differential Expression results from Limma or NanoStringDiff |
outputDir |
Directory for output files. If NULL (default), will return the stacked report instead of writing to a file. |
A stacked report containing statistics and gene expression profiles for genes contained in each cluster
data("ExamplePathways") data("ExampleResults") # Results from runLimmaAnalysis fgseaResults <- limmaToFGSEA(ExampleResults, gene.sets = ExamplePathways, min.set = 5, rank.by = "t") leadingEdge <- fgseaToLEdge(fgseaResults, cutoff.type = "padj", cutoff = 0.1) fgseaGrouped <- groupFGSEA(fgseaResults$Autoimmune.retinopathy, leadingEdge$Autoimmune.retinopathy, join.threshold = 0.5, dist.method = "binary") results.AR <- groupedGSEAtoStackedReport( fgseaGrouped, leadingEdge = leadingEdge$Autoimmune.retinopathy, de.fit = ExampleResults)