Significance-based Modules Integrating the Transcriptome and Epigenome


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Documentation for package ‘SMITE’ version 1.4.1

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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