makeFGSEAmasterTable: Make master table of all GSEA results

In calebclass/NanoTube: An Easy Pipeline for NanoString nCounter Data Analysis

Make master table of all GSEA results

Description

This function clusters GSEA results by leading edge similarity, and then combines to a data frame or text file.

Usage

makeFGSEAmasterTable(
  genesetResults,
  leadingEdge,
  join.threshold = 0.5,
  ngroups = NULL,
  dist.method = "binary",
  filename = NULL
)

Arguments

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.

Value

A table of GSEA results, clustered by similarity of leading edge.

calebclass/NanoTube documentation built on Nov. 21, 2023, 12:31 p.m.