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attract (version 1.24.0)

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

Description

This package contains the functions to find the gene expression modules that represent the drivers of Kauffman's attractor landscape. The modules are the core attractor pathways that discriminate between different cell types of groups of interest. Each pathway has a set of synexpression groups, which show transcriptionally-coordinated changes in gene expression.

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Version

Version

1.24.0

License

LGPL (>= 2.0)

Maintainer

Samuel Zimmerman

Last Published

February 15th, 2017

Functions in attract (1.24.0)

buildCustomIncidenceMatrix

This function builds an incidence matrix for custom gene sets.
filterDataSet

This function filters our lowly expressed genes in RNAseq data.
attract-package

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

Internal function - finds the synexpression groups for a single given pathway.
buildCorMatrix

Internal function - builds the correlation matrix between an average transcriptional module expression profile and a set of other genes.
SynExpressionSet-class

Class SynExpressionSet
findCorrPartners

Determines Genes with Highly Correlated Expression Profiles to a Synexpression Group
subset.loring.eset

An ExpressionSet Object containing published data from M?ller et al.
loring.eset

An ExpressionSet Object containing published data from M?ller et al.
removeFlatGenes

Flags a set of genes which demonstrates little variation across the celltypes or experimental groups of interest.
calcInform

Function calculates the informativeness metric (average MSS) for a set of cluster assignments.
AttractorModuleSet-class

Class AttractorModuleSet
buildKeggIncidenceMatrix

Internal function - buildings the KEGG incidence matrix requird by GSEAlm.
findSynexprs

This function finds the synexpression groups present within a core attractor pathway module.
samp.info

samp.info Contains the Sample Information for the Mueller data set.
getPwayGenes

Function removes genes from the chosen pathway that demonstrate little variation across the cell types.
calcFuncSynexprs

Functional enrichmental analysis for a set of synexpression groups.
exprs.dat

Gene Expression Matrix of Published Data
flagPwayExists

Internal function - flags a gene if it exists in a pathway.
calcRss

Function calculates the average RSS for a set of cluster assignments.
plotsynexprs

Visualizing the Average Expression Profile of a Synexpression Group.
calcModfstat

Function calculates a modified F-statistic for a set of cluster assignments.
findAttractors

Infers the set of cell-lineage specific gene expression modules using GSEAlm and KEGG.
getCustomGenes

Function removes genes from the custom pathway that demonstrate little variation across the cell types.