Significance-based Modules Integrating the Transcriptome and
Epigenome
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Documentation for package ‘SMITE’ version 1.30.0
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 |