pathVar: 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.

AuthorLaurence de Torrente, Samuel Zimmerman, Jessica Mar
Date of publicationNone
MaintainerSamuel Zimmerman <sezimmer@einstein.yu.edu>
LicenseLGPL (>= 2.0)
Version1.4.0

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...

Functions

bock Man page
diagnosticsVarPlots Man page
diagnosticsVarPlotsTwoSample Man page
geneDistributionSet Man page
geneDistributionSet2 Man page
geneDistributionSet2-class Man page
geneDistributionSet3 Man page
geneDistributionSet3-class Man page
geneDistributionSet-class Man page
geneSet Man page
geneSet-class Man page
getGenes Man page
makeDBList Man page
pathVar Man page
pathVarOneSample Man page
pathVar-package Man page
pathVarTwoSamplesCont Man page
pathVarTwoSamplesDisc Man page
plotAllTwoSampleDistributionCounts Man page
plotPway Man page
pways.kegg Man page
pways.reactome Man page
saveAsPDF Man page
significantPathway Man page
significantPathway2 Man page
significantPathway2-class Man page
significantPathway3 Man page
significantPathway3-class Man page
significantPathway-class Man page
sigPway Man page

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