AttractorModuleSet-class: Class AttractorModuleSet

In jmarlab/attract: Methods to Find the Gene Expression Modules that Represent the Drivers of Kauffman's Attractor Landscape

Description

This is a class representation for storing the output of the findAttractors function.

Objects from the Class

Objects are output by the function findAttractors. Objects can also be created by using new("AttractorModuleSet", ...).

Slots

eSet:

ExpressionSet which primarily stores the expression data and the phenotype/sample data sets.

cellTypeTag:

character string of the tag which stores the group membership information for the samples. Must be a column name of the data frame pData(eset).

incidenceMatrix:

incidence matrix used as input to GSEAlm.

rankedPathways:

Data frame of significantly enriched pathways, ranked first by significance and then by size.

Methods

No methods have yet been defined with class "AttractorModuleSet" in the signature.

Note

This class is better describe in the vignette.

Author(s)

Jessica Mar [e-mail]

Examples

## Not run: 
new.attractmodule <- new("AttractorModuleSet", eSet=new("ExpressionSet"), cellTypeTag=character(1), incidenceMatrix=matrix(0), rankedPathways=data.frame())

## End(Not run)

jmarlab/attract documentation built on May 23, 2019, 9:02 p.m.