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.

AuthorNeil Ari Wijetunga, Andrew Damon Johnston, John Murray Greally
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

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

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

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