fgseaPostprocessingXLSX {NanoTube} | R Documentation |
Clusters GSEA results by leading edge genes, and writes reports showing gene expression profiles of these genes (to Excel).
fgseaPostprocessingXLSX( genesetResults, leadingEdge, limmaResults, join.threshold = 0.5, ngroups = NULL, dist.method = "binary", filename )
genesetResults |
Results from pathway analysis using limmaToFGSEA. |
leadingEdge |
Results from fgseaToLEdge |
limmaResults |
Results from runLimmaAnalysis |
join.threshold |
The threshold distance to join gene sets. Gene sets with a distance below this value will be joined to a single "cluster." |
ngroups |
The desired number of gene set groups. Either 'join.threshold' or 'ngroups' must be specified, 'ngroups' takes priority if both are specified. |
dist.method |
Method for distance calculation (see options for dist()). We recommend the 'binary' (also known as Jaccard) distance. |
filename |
File name for the output Excel file. |
An Excel file where the first sheet summarizes the gene set analysis results. Subsequent sheets are reports showing differential expression statistics of leading edge genes.
data("ExamplePathways") data("ExampleResults") # Results from runLimmaAnalysis fgseaResults <- limmaToFGSEA(ExampleResults, gene.sets = ExamplePathways) leadingEdge <- fgseaToLEdge(fgseaResults, cutoff.type = "padj", cutoff = 0.1) fgseaPostprocessingXLSX(fgseaResults, leadingEdge, limmaResults = ExampleResults, join.threshold = 0.5, filename = "Results.xlsx")