Man pages for SMITE
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_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 |
