Methods to Find the Gene Expression Modules that Represent the Drivers of Kauffman's Attractor Landscape

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Documentation for package ‘attract’ version 1.60.0

• DESCRIPTION file.
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attract-package	Methods to find the Gene Expression Modules that Represent the Drivers of Kauffman's Attractor Landscape
attract	Methods to find the Gene Expression Modules that Represent the Drivers of Kauffman's Attractor Landscape
AttractorModuleSet	Class AttractorModuleSet
AttractorModuleSet-class	Class AttractorModuleSet
buildCustomIncidenceMatrix	This function builds an incidence matrix for custom gene sets.
calcFuncSynexprs	Functional enrichmental analysis for a set of synexpression groups.
calcInform	Function calculates the informativeness metric (average MSS) for a set of cluster assignments.
calcModfstat	Function calculates a modified F-statistic for a set of cluster assignments.
calcRss	Function calculates the average RSS for a set of cluster assignments.
exprs.dat	Gene Expression Matrix of Published Data
filterDataSet	This function filters our lowly expressed genes in RNAseq data.
findAttractors	Infers the set of cell-lineage specific gene expression modules using GSEAlm and KEGG.
findCorrPartners	Determines Genes with Highly Correlated Expression Profiles to a Synexpression Group
findSynexprs	This function finds the synexpression groups present within a core attractor pathway module.
loring.eset	An ExpressionSet Object containing published data from M?ller et al.
plotsynexprs	Visualizing the Average Expression Profile of a Synexpression Group.
removeFlatGenes	Flags a set of genes which demonstrates little variation across the celltypes or experimental groups of interest.
samp.info	samp.info Contains the Sample Information for the Mueller data set.
subset.loring.eset	An ExpressionSet Object containing published data from M?ller et al.
SynExpressionSet	Class SynExpressionSet
SynExpressionSet-class	Class SynExpressionSet