makeInputForEnrichmentMap: Wrapper to create input files for Enrichment Map

In BaderLab/netDx: Network-based patient classifier

Description

Wrapper to create input files for Enrichment Map

Usage

makeInputForEnrichmentMap(
  model,
  results,
  pathwayList,
  EMapMinScore = 0L,
  EMapMaxScore = 1L,
  EMapPctPass = 0.5,
  outDir
)

Arguments

model	(list) Output of training model, generated by running buildPredictor()
results	(list) Model results. output of getResults()
pathwayList	(list) output of readPathwayFile() used to make pathway-level feat ures for predictor
EMapMinScore	(integer) minimum score for Enrichment Map
EMapMaxScore	(integer) maximum score for Enrichment Map
EMapPctPass	(numeric between 0 and 1) percent of splits for which feature must have score in range [EMapMinScore,EMapMaxScore] to be included for EnrichmentMap visualization
outDir	(char) directory where files should be written

Details

An Enrichment Map is a network-based visualization of top-scoring pathway features and themes. It is generated in Cytoscape. This script generates the input files needed for Cytoscape to create an Enrichment Map visualization.

BaderLab/netDx documentation built on Sept. 26, 2021, 9:13 a.m.