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 |
| depends | base (>= 3.2.2) , ggplot2 , gridExtra , methods , R (>= 3.2.2) |
| imports | data , data.table , EMT , Matching , mclust |
| Contributors | Jessica Mar, Laurence Torrente, Samuel Zimmerman |
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