# Methods to Find Pathways with Significantly Different Variability

## Documentation for package ‘pathVar’ version 1.8.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

pathVar-package | Detects pathways with different levels of variance than reference gene set variability.
bock | Gene Expression Matrix of Published Data
diagnosticsVarPlots | Plots the average expression against variability using different summary statistics.
diagnosticsVarPlotsTwoSample | Plots the average expression against variability using different summary statistics when comparing 2 groups of samples to each other.
geneDistributionSet | Class '"geneDistributionSet"'
geneDistributionSet-class | Class '"geneDistributionSet"'
geneDistributionSet2 | Class '"pathVarTwoSamplesCont"'
geneDistributionSet2-class | Class '"pathVarTwoSamplesCont"'
geneDistributionSet3 | Class '"pathVarTwoSamplesDisc"'
geneDistributionSet3-class | Class '"pathVarTwoSamplesDisc"'
geneSet | Class '"geneSet"'
geneSet-class | Class '"geneSet"'
getGenes | Gets significant genes within a certain window of variability.
makeDBList | Puts your own list of pathways and genes related to them into a list.
pathVar | Detects pathways with different levels of variance than reference gene set variability.
pathVarOneSample | Compares the distribution of genes in each cluster to the distribution of genes in each cluster for every pathway.
pathVarTwoSamplesCont | Compares the distribution of genes in each pathway for two groups of samples that you define.
pathVarTwoSamplesDisc | Compares the number of genes in clusters in each pathway for two groups of samples that you define.
plotAllTwoSampleDistributionCounts | Compares the distribution of genes in clusters for every gene in your data set for two groups of samples that you define and plot the counts.
plotPway | Checks if an object is from the one sample or two samples cases and then plots reference distribution and the chosen pathway.
pways.kegg | List containing pathway IDs, names, and genes in each pathway
pways.reactome | List containing pathway IDs, names, and genes in each pathway
saveAsPDF | Save the plots of the significant pathway or a chosen list of pathways as a pdf.
significantPathway | Class '"significantPathway"'
significantPathway-class | Class '"significantPathway"'
significantPathway2 | Class '"significantPathway2"'
significantPathway2-class | Class '"significantPathway2"'
significantPathway3 | Class '"significantPathway3"'
significantPathway3-class | Class '"significantPathway3"'
sigPway | A function checks if an object is from the one sample or two samples cases and then finds the significant pathways.