Methods to Find Pathways with Significantly Different Variability

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Documentation for package ‘pathVar’ version 1.23.0

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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.