monsterAnalysis-class: Class "monsterAnalysis" - a list containing the transition...

In QuackenbushLab/MONSTER: Modeling Network State Transitions from Expression and Regulatory data (MONSTER)

Description

This is the main class for MONSTER.

Extends

Class list

Methods

Class-specific methods.

transitionNetworkPlot plots the transition matrix using the igraph library

transitionPCAPlot plots the transcription factors in the transition matrix along the top principal components

dTFIPlot plots the differential transcription factor involvement for each transcription factor against the distribution under the null

calculate.tm.p.values computes the significance of each transcription factor involvement.

hcl.heatmap.plot plots the transition matrix as a heatmap

Note

Note: This is a summary for reference. For an explanation of the actual usage, see the vignette.

'monsterAnalysis' obj are the main class in use by the MONSTER package. The class extends list and provides the key results from the results of the MONSTER analysis.

The transition matrix from the MONSTER analysis is contained in slot 'tm'. This slot contains an m by m square matrix representing the main observed result from the monster method.

For permutation testing, the slot 'nullTM' contains a list of matrices. The list has length equal to the given number of permutations run with monster

Data parameters, numGenes and numSamples indicate the number of genes and number of samples on which monster was originally run.

Examples

    # See vignette

QuackenbushLab/MONSTER documentation built on Oct. 22, 2020, 8:07 a.m.