pipe.GeneSetEnrichment: Gene Module and Pathway Enrichment

In robertdouglasmorrison/DuffyTools: Duffy Lab Utility Tools

Gene Module and Pathway Enrichment

Description

Submit Differential Expression (DE) Results to Pathway and Gene Module Enrichment Analysis

Usage

pipe.GeneSetEnrichment(sampleIDset, speciesID = "Pf3D7", annotationFile = "Annotation.txt", 
		optionsFile = "Options.txt", results.path = NULL, folderName = "", 
		toolName = c("MetaResults", "RoundRobin", "RankProduct", "SAM", "EdgeR", "DESeq"), 
		geneColumn = if (speciesID 
		groupColumn = "Group", 
		geneSets = c("GO.BiologicalProcess", "GO.MolecularFunction", "GO.CellularComponent", 
		"KEGG.Pathways", "MetabolicPathways", "GeneProduct", "PBMC.GeneModules", "Blood.GeneModules"), 
		descriptor = "Enrichment", maxPvalue = 0.05, wt.enrich = 1, wt.pvalue = 2, verbose = TRUE)

Arguments

sampleIDset	character vector of one or more SampleIDs
speciesID	the one SpeciesID of results to operate on
results.path	top level folder holding all results, by default taken from the Options Table
folderName	the named subfolder of DE results to operate on, without any species prefix
toolName	the one DE tool of results to operate on. Note that the quartet results.path, toolName, speciesID, folderName all combine to specify the exact absolute path to the DE results files that will be used as input.
geneColumn	the name of the column in the various DE results files that contains the GeneID terms contained in the geneSets. Note that this can vary from species to species
groupColumn	the name of the column in the Annotation Table that contains the names of the conditions that were used for differential expression (DE) analysis. Note that this determines the specific filenames of DE results that will be used as input.
geneSets	Either a chracter vector of pre-defined gene sets, or a list of gene sets where each elements name is a pathway/module and each element is a vector of GeneIDs from the given SpeciesID.
descriptor	a character string of length 1, that will be the name of the created subfolder of enrichment results
maxPvalue	P-value cutoff, to only report pathways/modules that have significant enrichment
wt.enrich	the relative weight to give to the enrichment magnitudes, for row-ordering the final results.
wt.pvalue	the relative weight to give to the enrichment P-values, for row-ordering the final results.

Details

This function takes a folder of Differential Expression results, and searches for interesting pathways and gene modules using the probability-based notion of enrichment. See the basics about enrichment at enrichment, and a lower level intermediate function geneSetEnrichment.

Whereas the enrichment primitive requires a fixed number of genes as input, this function chooses a family of gene counts, calls enrichment for each, and summarizes the results as per metaRank.data.frames.

Value

An entire subfolder of results is created, underneath the folder that contains all the results used as input. For each group named by groupColumn, an HTML file of enriched (up-regulated) pathways and/or gene modules that are significantly over-represented in the DE results for that group of samples.

Author(s)

Bob Morrison

See Also

pipe.GeneSetAnalysis for a similar idea of finding DE pathways and gene modules, but based on a completely different heuristic.

robertdouglasmorrison/DuffyTools documentation built on April 16, 2024, 6:31 a.m.