SMITE: Significance-based Modules Integrating the Transcriptome and Epigenome

Share:

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.

Author
Neil Ari Wijetunga, Andrew Damon Johnston, John Murray Greally
Date of publication
None
Maintainer
Neil Ari Wijetunga <Neil.Wijetunga@med.einstein.yu.edu>, Andrew Damon Johnston <Andrew.Johnston@med.einstein.yu.edu>
License
GPL (>=2)
Version
1.2.0
URLs

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

Files in this package

SMITE/DESCRIPTION
SMITE/NAMESPACE
SMITE/R
SMITE/R/AllClasses.R
SMITE/R/SMITE-generics.R
SMITE/R/SMITE-internal.R
SMITE/R/SMITE-plot.R
SMITE/R/SMITE-print.R
SMITE/R/SMITE-show.R
SMITE/R/SMITE.R
SMITE/build
SMITE/build/vignette.rds
SMITE/data
SMITE/data/Reactome.Symbol.Igraph.rda
SMITE/data/curated_expressiondata.rda
SMITE/data/datalist
SMITE/data/genes_for_conversiontest.rda
SMITE/data/hg19_genes_bed.rda
SMITE/data/histone_h3k4me1.rda
SMITE/data/methylationdata.rda
SMITE/data/test_annotation_score_data.rda
SMITE/inst
SMITE/inst/NEWS
SMITE/inst/doc
SMITE/inst/doc/SMITE.R
SMITE/inst/doc/SMITE.Rmd
SMITE/inst/doc/SMITE.pdf
SMITE/inst/extdata
SMITE/inst/extdata/hg19_symbol_hpaii.sites.inbodyand2kbupstream.bed.gz
SMITE/man
SMITE/man/Reactome.Symbol.Igraph.Rd
SMITE/man/SMITE-package.Rd
SMITE/man/addShadowText.Rd
SMITE/man/annotateExpression.Rd
SMITE/man/annotateModification.Rd
SMITE/man/convertGeneIds.Rd
SMITE/man/curated_expression.Rd
SMITE/man/extractExpression.Rd
SMITE/man/extractGOseq.Rd
SMITE/man/extractModification.Rd
SMITE/man/extractModules.Rd
SMITE/man/extractScores.Rd
SMITE/man/genes_for_conversiontest.Rd
SMITE/man/hg19_gene_bed.Rd
SMITE/man/highScores.Rd
SMITE/man/histone_h3k4me1.Rd
SMITE/man/makePvalueAnnotation.Rd
SMITE/man/makePvalueObject.Rd
SMITE/man/methylationdata.Rd
SMITE/man/normalizePval.Rd
SMITE/man/plotCompareScores.Rd
SMITE/man/plotDensityPval.Rd
SMITE/man/plotModule.Rd
SMITE/man/removeModification.Rd
SMITE/man/runBioNet.Rd
SMITE/man/runGOseq.Rd
SMITE/man/runSpinglass.Rd
SMITE/man/scorePval.Rd
SMITE/man/stoufferTest.Rd
SMITE/man/test_annotation_score_data.Rd
SMITE/vignettes
SMITE/vignettes/SMITE.Rmd