Man pages for Bioconductor-mirror/SMITE
Significance-based Modules Integrating the Transcriptome and Epigenome

addShadowTextAdd shadow text (a second color bordering the text) to a plot
annotateExpressionAdding expression data to a PvalueAnnotation
annotateModificationAdding modification data to a PvalueAnnotation
convertGeneIdsConvert between gene ids
curated_expressionA toy dataset ofcurated RNA-seq to test within SMITE
extractExpressionView the expression data stored in a PvalueAnnotation
extractGOseqView the GOseq pathway analysis after having run Goseq, or...
extractModificationExtract some or all loaded modifications or a the summary of...
extractModulesView specific modules within a PvalueAnnotation
extractScoresExtract scores for all genes
genes_for_conversiontestA small set of RefSeq genes for converting
hg19_gene_bedA bed file annotating Refseq genes for the hg19 genome build
highScoresGenerate a vector of the highest scoring genes
histone_h3k4me1A toy dataset of H3k4me1 peaks to test within SMITE
makePvalueAnnotationInitialize a PvalueAnnotation
makePvalueObjectFunction to make a PvalueObject within a PvalueAnnotation
methylationdataA toy dataset of DNA methylation to test within SMITE
normalizePvalThis function normalizes p-values (Scores) that are otherwise...
plotCompareScoresCompare two genomic features by score and display them in a...
plotDensityPvalPlot the density of the combined scores stored in a...
plotModulePlot a specific module after running Spinglass algorithm
Reactome.Symbol.IgraphAn Igraph network for REACTOME with nodes as gene symbols
removeModificationA function to "unload" a modification that has already been...
runBioNetPerform BioNet Analysis on a PvalueAnnotation
runGOseqRun a GoSeq pathway analysis
runSpinglassRun Spinglass algorithm on a Scored PvalueAnnotation
scorePvalMaking a single combined score for each gene
SMITE-packageSignificance-based Modules Integrating the Transcriptome and...
stoufferTestStouffer's Test
test_annotation_score_dataA toy PvalueAnnotation
Bioconductor-mirror/SMITE documentation built on Aug. 12, 2017, 5:11 p.m.