pipe.GeneSetAnalysis: Pathway and Gene Module Analysis

In robertdouglasmorrison/DuffyTools: Duffy Lab Utility Tools

Pathway and Gene Module Analysis

Description

Look for differentially expressed (DE) Pathways and Gene Modules from differential gene expression results.

Usage

pipe.GeneSetAnalysis(sampleIDset, speciesID = "Pf3D7", annotationFile = "Annotation.txt", 
	optionsFile = "Options.txt", results.path = NULL, folderName = "", 
	toolName = c("MetaResults", "RoundRobin", "RankProduct", "SAM", "DESeq", "EdgeR"), 
	geneMapColumn = if (speciesID 
	groupColumn = "Group", colorColumn = "Color", 
	geneSets = c("GO.BiologicalProcess", "GO.MolecularFunction", "GO.CellularComponent", 
	"KEGG.Pathways", "MetabolicPathways", "GeneProduct", "PBMC.GeneModules", "Blood.GeneModules"), 
	descriptor = "GeneSets", minGenesPerSet = if (speciesID 
	mode = c("combined", "separate"), cutPvalue = 0.01, verbose = T)

Arguments

sampleIDset	character vector of 2 or more SampleIDs. This selects which groups/conditions are to be analysed.
speciesID	the species (organism) being evaluated
results.path	top level folder of results, defaults to the value in the Options table
folderName	the name of the subfolder of DE comparisons to use
toolName	the name of the DE tool used to generate the differential gene expression results.
geneMapColumn	the name of the column in the current species' GeneMap that contains the GeneIDs found in the GeneSets. Some species use full notation GeneIDs and others uses simpler gene symbols.
groupColumn	the name of one column in the Annotation table, that specifies the group/condition for each sample.
colorColumn	the name of one column in the Annotation table, that specifies the color to use for each group/condition.
geneSets	either a character vector of names of pre-defined GeneSet objects, or a list of vectors of GeneIDs.
descriptor	a character string for naming the final folder of created analyses.
minGenesPerSet	the minimum number of genes that a GeneSet can contain. Very low count sets are ignored.
mode	how to treat the various geneSets, whether to combine them all into one folder of joint analysis, or to evaluate each GeneSet separately in its own subfolder.
cutPvalue	maximum P-value to include a GeneSet in the final results. Lowering the P-value will produce less results.

Details

This function analyzes how pre-defined sets of genes are differentially expressed between 2 or more conditions. The methodology is to treat each gene as a point mass, located at its rank order location in each of the condition's DE results, and then summarize all the genes in each GeneSet as a density mass for the set. A gene set is called differentially expressed in a condition if its density mass is significantly shifted with respect to that same gene set in all other conditions.

Value

A folder of results, where the final name/location is a combination of results.path, toolName, speciesID, folderName, descriptor.

In that folder will be a family of HTML files for each condition, one HTML and .txt file ocvering all GeneSets and conditions, and a subfolder of all plots and hyperlinked gene/module files.

Briefly, for each condition, there are HTML files for the most up-regulated and down-regulated GeneSets, with P-values and density rank shifts for each significantly DE GeneSet. Within each HTML file are links to images of density plots for each GeneSet, and to gene membership tables to examine the details about genes in that GeneSet.

Author(s)

Bob Morrison

See Also

pipe.GeneSetEnrichment for a similar function based on enrichment instead of mass density. geneSetAnalysis for the lower-lever function using lists instead of SampleIDs.

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