makeFGSEAmasterTable {NanoTube} | R Documentation |
This function clusters GSEA results by leading edge similarity, and then combines to a data frame or text file.
makeFGSEAmasterTable( genesetResults, leadingEdge, join.threshold = 0.5, ngroups = NULL, dist.method = "binary", filename = NULL )
genesetResults |
Results from pathway analysis using limmaToFGSEA. |
leadingEdge |
Results from fgseaToLEdge |
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 text file. If NULL (default), data will be returned as an R data frame. |
A table of GSEA results, clustered by similarity of leading edge.