geneSetAnalysis: Pathway and Gene Set Analysis using Density Curves

In robertdouglasmorrison/DuffyTools: Duffy Lab Utility Tools

Pathway and Gene Set Analysis using Density Curves

Description

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

Usage

geneSetDensity(deList, geneSets, speciesID = getCurrentSpecies(), colorset = c(2:(length(deList) + 1)), 
	optionsFile = "Options.txt", results.path = NULL, folderName = "", 
	toolName = c("MetaResults", "RoundRobin", "RankProduct", "SAM", "DESeq", "EdgeR"), 
	descriptor = "GeneSet", minGenesPerSet = 2, trimGenesToGeneMap = TRUE,
	geneMapColumn = if (speciesID 
	cutPvalue = 0.05, cutRankShift = NULL, cutFold = 0.1, cutFDR = 0.05,
	makePlots = TRUE, PLOT.FUN = NULL, makeGeneTables = TRUE,
	doFDR = TRUE, NgeneSets = 500)

Arguments

deList	a named list of differential expression (DE) data frames (2 or more), containing the DE results for each condition. The names of the list should be the names of the conditions.
geneSets	either a character vector of names of pre-defined GeneSet objects, or a list of vectors of GeneIDs.
speciesID	the species (organism) being evaluated
colorset	a vector of colors for displaying each condition
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.
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.
trimGenesToGeneMap	logical, removes extra gene terms from any gene set references that are not in the current gene map.
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.
cutPvalue	maximum P-value to include a GeneSet in the final results. Lowering the P-value will produce less results.
cutRankShift	minimum rank shift to include a GeneSet in the final results. Raising the ranks shift will produce less results.
cutFold	minimum fold change to include a GeneSet in the final results. Raising the fold change will produce less results.
cutFDR	maximum FDR to include a GeneSet in the final results. Lowering the FDR will produce less results. Only used when doFDR=TRUE.
doFDR	logical, should a False Discovery Rate be calculated, and added to all results. Rather slow.
makePlots	logical, should plot images for each GeneSet be created
PLOT.FUN	optional function to be called for making gene set plots. Must take one argument that is a vector of gene IDs.
makeGeneTables	logical, should small HTML files of gene-to-GeneSet membership tables be created

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

geneSetEnrichment for a similar function based on enrichment instead of mass density. pipe.GeneSetAnalysis for a high-lever wrapper function using SampleIDs.

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