Learn R Programming

pathVar (version 1.2.0)

Methods to Find Pathways with Significantly Different Variability

Description

This package contains the functions to find the pathways that have significantly different variability than a reference gene set. It also finds the categories from this pathway that are significant where each category is a cluster of genes. The genes are separated into clusters by their level of variability.

Copy Link

Version

Version

1.2.0

License

LGPL (>= 2.0)

Maintainer

Samuel Zimmerman

Last Published

February 15th, 2017

Functions in pathVar (1.2.0)

geneDistributionSet-class

Class "geneDistributionSet"
geneSet-class

Class "geneSet"
pathVar-package

Detects pathways with different levels of variance than reference gene set variability.
getGenes

Gets significant genes within a certain window of variability.
geneDistributionSet3-class

Class "pathVarTwoSamplesDisc"
geneDistributionSet2-class

Class "pathVarTwoSamplesCont"
makeDBList

Puts your own list of pathways and genes related to them into a list.
pathVarOneSample

Compares the distribution of genes in each cluster to the distribution of genes in each cluster for every pathway.
bock

Gene Expression Matrix of Published Data
diagnosticsVarPlots

Plots the average expression against variability using different summary statistics.
plotPway

Checks if an object is from the one sample or two samples cases and then plots reference distribution and the chosen pathway.
significantPathway3-class

Class "significantPathway3"
saveAsPDF

Save the plots of the significant pathway or a chosen list of pathways as a pdf.
pathVarTwoSamplesCont

Compares the distribution of genes in each pathway for two groups of samples that you define.
significantPathway-class

Class "significantPathway"
significantPathway2-class

Class "significantPathway2"
pathVarTwoSamplesDisc

Compares the number of genes in clusters in each pathway for two groups of samples that you define.
pways.reactome

List containing pathway IDs, names, and genes in each pathway
sigPway

A function checks if an object is from the one sample or two samples cases and then finds the significant pathways.
pways.kegg

List containing pathway IDs, names, and genes in each pathway