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. |
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. |
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. |