SMITE: Significance-based Modules Integrating the Transcriptome and Epigenome

This package builds on the Epimods framework which facilitates finding weighted subnetworks ("modules") on Illumina Infinium 27k arrays using the SpinGlass algorithm, as implemented in the iGraph package. We have created a class of gene centric annotations associated with p-values and effect sizes and scores from any researchers prior statistical results to find functional modules.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("SMITE")
AuthorNeil Ari Wijetunga, Andrew Damon Johnston, John Murray Greally
Bioconductor views Coverage DifferentialExpression DifferentialMethylation GenomeAnnotation Network NetworkEnrichment RNASeq Sequencing SystemsBiology
Date of publicationNone
MaintainerNeil Ari Wijetunga <Neil.Wijetunga@med.einstein.yu.edu>, Andrew Damon Johnston <Andrew.Johnston@med.einstein.yu.edu>
LicenseGPL (>=2)
Version1.2.0
https://github.com/GreallyLab/SMITE

View on Bioconductor

Man pages

addShadowText: Add shadow text (a second color bordering the text) to a plot

annotateExpression: Adding expression data to a PvalueAnnotation

annotateModification: Adding modification data to a PvalueAnnotation

convertGeneIds: Convert between gene ids

curated_expression: A toy dataset ofcurated RNA-seq to test within SMITE

extractExpression: View the expression data stored in a PvalueAnnotation

extractGOseq: View the GOseq pathway analysis after having run Goseq, or...

extractModification: Extract some or all loaded modifications or a the summary of...

extractModules: View specific modules within a PvalueAnnotation

extractScores: Extract scores for all genes

genes_for_conversiontest: A small set of RefSeq genes for converting

hg19_gene_bed: A bed file annotating Refseq genes for the hg19 genome build

highScores: Generate a vector of the highest scoring genes

histone_h3k4me1: A toy dataset of H3k4me1 peaks to test within SMITE

makePvalueAnnotation: Initialize a PvalueAnnotation

makePvalueObject: Function to make a PvalueObject within a PvalueAnnotation

methylationdata: A toy dataset of DNA methylation to test within SMITE

normalizePval: This function normalizes p-values (Scores) that are otherwise...

plotCompareScores: Compare two genomic features by score and display them in a...

plotDensityPval: Plot the density of the combined scores stored in a...

plotModule: Plot a specific module after running Spinglass algorithm

Reactome.Symbol.Igraph: An Igraph network for REACTOME with nodes as gene symbols

removeModification: A function to "unload" a modification that has already been...

runBioNet: Perform BioNet Analysis on a PvalueAnnotation

runGOseq: Run a GoSeq pathway analysis

runSpinglass: Run Spinglass algorithm on a Scored PvalueAnnotation

scorePval: Making a single combined score for each gene

SMITE-package: Significance-based Modules Integrating the Transcriptome and...

stoufferTest: Stouffer's Test

test_annotation_score_data: A toy PvalueAnnotation

Functions

addShadowText Man page
addShadowText,ANY-method Man page
annotateExpression Man page
annotateExpression,PvalueAnnotation-method Man page
annotateModification Man page
annotateModification,PvalueAnnotation-method Man page
convertGeneIds Man page
convertGeneIds,character,character,character-method Man page
curated_expressiondata Man page
expression_curated Man page
extractExpression Man page
extractExpression,PvalueAnnotation-method Man page
extractGOseq Man page
extractGOseq,PvalueAnnotation-method Man page
extractModification Man page
extractModification,PvalueAnnotation-method Man page
extractModSummary Man page
extractModSummary,PvalueAnnotation-method Man page
extractModules Man page
extractModules,PvalueAnnotation-method Man page
extractScores Man page
extractScores,PvalueAnnotation-method Man page
genes Man page
genes_for_conversiontest Man page
h3k4me1 Man page
hg19_genes Man page
hg19_genes_bed Man page
highScores Man page
highScores,PvalueAnnotation-method Man page
histone_h3k4me1 Man page
makePvalueAnnotation Man page
makePvalueAnnotation,ANY-method Man page
makePvalueObject Man page
makePvalueObject,PvalueAnnotation-method Man page
methylation Man page
methylationdata Man page
normalizePval Man page
normalizePval,PvalueAnnotation-method Man page
plotCompareScores Man page
plotCompareScores,PvalueAnnotation-method Man page
plotDensityPval Man page
plotDensityPval,PvalueAnnotation-method Man page
plotModule Man page
plotModule,PvalueAnnotation-method Man page
REACTOME Man page
Reactome.Symbol.Igraph Man page
removeModification Man page
removeModification,PvalueAnnotation-method Man page
runBioNet Man page
runBioNet,PvalueAnnotation-method Man page
runGOseq Man page
runGOseq,PvalueAnnotation-method Man page
runSpinglass Man page
runSpinglass,PvalueAnnotation-method Man page
scorePval Man page
scorePval,PvalueAnnotation-method Man page
searchGOseq Man page
searchGOseq,PvalueAnnotation-method Man page
SMITE Man page
SMITE-package Man page
stoufferTest Man page
stoufferTest,vector-method Man page
test_annotation Man page
test_annotation_score_data Man page

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.