pathVar: Methods to Find Pathways with Significantly Different Variability

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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.

Author
Laurence de Torrente, Samuel Zimmerman, Jessica Mar
Date of publication
None
Maintainer
Samuel Zimmerman <sezimmer@einstein.yu.edu>
License
LGPL (>= 2.0)
Version
1.4.0

View on Bioconductor

Man pages

bock
Gene Expression Matrix of Published Data
diagnosticsVarPlots
Plots the average expression against variability using...
diagnosticsVarPlotsTwoSample
Plots the average expression against variability using...
geneDistributionSet2-class
Class '"pathVarTwoSamplesCont"'
geneDistributionSet3-class
Class '"pathVarTwoSamplesDisc"'
geneDistributionSet-class
Class '"geneDistributionSet"'
geneSet-class
Class '"geneSet"'
getGenes
Gets significant genes within a certain window of...
makeDBList
Puts your own list of pathways and genes related to them into...
pathVarOneSample
Compares the distribution of genes in each cluster to the...
pathVar-package
Detects pathways with different levels of variance than...
pathVarTwoSamplesCont
Compares the distribution of genes in each pathway for two...
pathVarTwoSamplesDisc
Compares the number of genes in clusters in each pathway for...
plotAllTwoSampleDistributionCounts
Compares the distribution of genes in clusters for every gene...
plotPway
Checks if an object is from the one sample or two samples...
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...
significantPathway2-class
Class '"significantPathway2"'
significantPathway3-class
Class '"significantPathway3"'
significantPathway-class
Class '"significantPathway"'
sigPway
A function checks if an object is from the one sample or two...

Files in this package

pathVar/DESCRIPTION
pathVar/NAMESPACE
pathVar/NEWS
pathVar/R
pathVar/R/classdef.R
pathVar/R/pipeline.final.R
pathVar/build
pathVar/build/vignette.rds
pathVar/data
pathVar/data/bock.RData
pathVar/data/pways.kegg.RData
pathVar/data/pways.reactome.RData
pathVar/inst
pathVar/inst/CITATION
pathVar/inst/doc
pathVar/inst/doc/pathVar.R
pathVar/inst/doc/pathVar.Rnw
pathVar/inst/doc/pathVar.pdf
pathVar/man
pathVar/man/bock.Rd
pathVar/man/diagnosticsVarPlots.Rd
pathVar/man/diagnosticsVarPlotsTwoSample.Rd
pathVar/man/geneDistributionSet-class.Rd
pathVar/man/geneDistributionSet2-class.Rd
pathVar/man/geneDistributionSet3-class.Rd
pathVar/man/geneSet-class.Rd
pathVar/man/getGenes.Rd
pathVar/man/makeDBList.Rd
pathVar/man/pathVar-package.Rd
pathVar/man/pathVarOneSample.Rd
pathVar/man/pathVarTwoSamplesCont.Rd
pathVar/man/pathVarTwoSamplesDisc.Rd
pathVar/man/plotAllTwoSampleDistributionCounts.Rd
pathVar/man/plotPway.Rd
pathVar/man/pways.kegg.Rd
pathVar/man/pways.reactome.Rd
pathVar/man/saveAsPDF.Rd
pathVar/man/sigPway.Rd
pathVar/man/significantPathway-class.Rd
pathVar/man/significantPathway2-class.Rd
pathVar/man/significantPathway3-class.Rd
pathVar/vignettes
pathVar/vignettes/outline_fig_2.pdf
pathVar/vignettes/pathVar.Rnw