# Significance-based Modules Integrating the Transcriptome and Epigenome

## Documentation for package ‘SMITE’ version 1.6.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

SMITE-package | Significance-based Modules Integrating the Transcriptome and Epigenome
addShadowText | Add shadow text (a second color bordering the text) to a plot
addShadowText-method | Add shadow text (a second color bordering the text) to a plot
annotateExpression | Adding expression data to a PvalueAnnotation
annotateExpression-method | Adding expression data to a PvalueAnnotation
annotateModification | Adding modification data to a PvalueAnnotation
annotateModification-method | Adding modification data to a PvalueAnnotation
convertGeneIds | Convert between gene ids
convertGeneIds-method | Convert between gene ids
curated_expressiondata | A toy dataset ofcurated RNA-seq to test within SMITE
expression_curated | A toy dataset ofcurated RNA-seq to test within SMITE
extractExpression | View the expression data stored in a PvalueAnnotation
extractExpression-method | View the expression data stored in a PvalueAnnotation
extractGOseq | View the GOseq pathway analysis after having run Goseq, or search for a term.
extractGOseq-method | View the GOseq pathway analysis after having run Goseq, or search for a term.
extractModification | Extract some or all loaded modifications or a the summary of combined effects
extractModification-method | Extract some or all loaded modifications or a the summary of combined effects
extractModSummary | Extract some or all loaded modifications or a the summary of combined effects
extractModSummary-method | Extract some or all loaded modifications or a the summary of combined effects
extractModules | View specific modules within a PvalueAnnotation
extractModules-method | View specific modules within a PvalueAnnotation
extractScores | Extract scores for all genes
extractScores-method | Extract scores for all genes
genes | A small set of RefSeq genes for converting
genes_for_conversiontest | A small set of RefSeq genes for converting
h3k4me1 | A toy dataset of H3k4me1 peaks to test within SMITE
hg19_genes | A bed file annotating Refseq genes for the hg19 genome build
hg19_genes_bed | A bed file annotating Refseq genes for the hg19 genome build
highScores | Generate a vector of the highest scoring genes
highScores-method | Generate a vector of the highest scoring genes
histone_h3k4me1 | A toy dataset of H3k4me1 peaks to test within SMITE
makePvalueAnnotation | Initialize a PvalueAnnotation
makePvalueAnnotation-method | Initialize a PvalueAnnotation
makePvalueObject | Function to make a PvalueObject within a PvalueAnnotation
makePvalueObject-method | Function to make a PvalueObject within a PvalueAnnotation
methylation | A toy dataset of DNA methylation to test within SMITE
methylationdata | A toy dataset of DNA methylation to test within SMITE
normalizePval | This function normalizes p-values (Scores) that are otherwise on different scales.
normalizePval-method | This function normalizes p-values (Scores) that are otherwise on different scales.
plotCompareScores | Compare two genomic features by score and display them in a hexbin plot
plotCompareScores-method | Compare two genomic features by score and display them in a hexbin plot
plotDensityPval | Plot the density of the combined scores stored in a PvalueObject
plotDensityPval-method | Plot the density of the combined scores stored in a PvalueObject
plotModule | Plot a specific module after running Spinglass algorithm
plotModule-method | Plot a specific module after running Spinglass algorithm
REACTOME | An Igraph network for REACTOME with nodes as gene symbols
Reactome.Symbol.Igraph | An Igraph network for REACTOME with nodes as gene symbols
removeModification | A function to "unload" a modification that has already been added.
removeModification-method | A function to "unload" a modification that has already been added.
runBioNet | Perform BioNet Analysis on a PvalueAnnotation
runBioNet-method | Perform BioNet Analysis on a PvalueAnnotation
runGOseq | Run a GoSeq pathway analysis
runGOseq-method | Run a GoSeq pathway analysis
runSpinglass | Run Spinglass algorithm on a Scored PvalueAnnotation
runSpinglass-method | Run Spinglass algorithm on a Scored PvalueAnnotation
scorePval | Making a single combined score for each gene
scorePval-method | Making a single combined score for each gene
searchGOseq | View the GOseq pathway analysis after having run Goseq, or search for a term.
searchGOseq-method | View the GOseq pathway analysis after having run Goseq, or search for a term.
SMITE | Significance-based Modules Integrating the Transcriptome and Epigenome
stoufferTest | Stouffer's Test
stoufferTest-method | Stouffer's Test
test_annotation | A toy PvalueAnnotation
test_annotation_score_data | A toy PvalueAnnotation