Reactome.Symbol.Igraph
                        An Igraph network for REACTOME with nodes as
                        gene symbols
SMITE-package           Significance-based Modules Integrating the
                        Transcriptome and Epigenome
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_expressiondata
                        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 search for a term.
extractModification     Extract some or all loaded modifications or a
                        the summary of combined effects
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_genes_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 on different scales.
plotCompareScores       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
plotModule              Plot a specific module after running Spinglass
                        algorithm
removeModification      A function to "unload" a modification that has
                        already been added.
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
stoufferTest            Stouffer's Test
test_annotation_score_data
                        A toy PvalueAnnotation
