pathVar v1.2.0

Methods to Find Pathways with Significantly Different Variability

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.

Functions in pathVar

Name Description
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
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Details

Type Package
Date 2016-02-09
License LGPL (>= 2.0)
Collate classdef.R pipeline.final.R
LazyData true
biocViews GeneticVariability, GeneSetEnrichment, Pathways
NeedsCompilation no

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