Man pages for ELMER
Inferring Regulatory Element Landscapes and Transcription Factor Networks Using Cancer Methylomes
| addDistNearestTSS | Calculate the distance between probe and gene TSS |
| addMutCol | Adds mutation information to MAE |
| calcDistNearestTSS | Calculate distance from region to nearest TSS |
| calculateEnrichement | Calculate motif Erichment |
| createBigWigDNAmetArray | Create a bigwig file for IGV visualization of DNA methylation... |
| createIGVtrack | Create a junction track for IGV visualization of interection |
| createMAE | Construct a Multi Assay Experiment for ELMER analysis |
| createMotifRelevantTfs | Get family of transcription factors |
| createSummaryDocument | Create summary document for TCGA.pipe function |
| createTSVTemplates | Create examples files for Sample mapping and information used... |
| ELMER | ELMER (Enhancer Linking by Methylation/Expression... |
| findMotifRegion | Use Hocomoco motif and homer to identify motifs in a given... |
| get450K | get450K to download HM40K DNA methylation data for certain... |
| getClinic | getClinic to download clinic data for certain cancer types... |
| get.diff.meth | Identify hypo/hyper-methylated CpG sites between two groups... |
| get.enriched.motif | get.enriched.motif to identify the overrepresented motifs in... |
| getExp | Get Gene expression object from MAE |
| getExpSamples | Get Gene expression object samples from MAE |
| get.feature.probe | get.feature.probe to select probes within promoter regions or... |
| getGeneID | getGeneID to report gene id from symbol |
| getMet | Get DNA methylation object from MAE |
| getMetSamples | Get DNA methylation object samples from MAE |
| GetNearGenes | GetNearGenes to collect nearby genes for one locus. |
| get.pair | get.pair to predict enhancer-gene linkages. |
| get.permu | get.permu to generate permutation results for calculation of... |
| Get.Pvalue.p | Calculate empirical Pvalue |
| getRandomPairs | Get random pairs |
| getRegionNearGenes | Identifies nearest genes to a region |
| getRNAseq | getRNAseq to download all RNAseq data for a certain cancer... |
| getSymbol | getSymbol to report gene symbol from id |
| get.tab | summarize MR TF as a binary table with 1 if TF was found in... |
| get.tabs | Creating matrix for MR TF heatmap |
| getTCGA | getTCGA to download DNA methylation, RNA expression and... |
| getTF | Get human TF list from the UNiprot database |
| getTFBindingSites | Get MR TF binding regions infered by ELMER |
| get.TFs | get.TFs to identify regulatory TFs. |
| getTFtargets | Get TF target genes |
| getTSS | getTSS to fetch GENCODE gene annotation (transcripts level)... |
| heatmapGene | Heatmap for correlation between probes DNA methylation and a... |
| heatmapPairs | Heatmap of pairs gene and probes anti-correlated |
| lm_eqn | lable linear regression formula |
| metBoxPlot | scatter.plot to plot scatter plots between gene expression... |
| motif.enrichment.plot | motif.enrichment.plot to plot bar plots showing motif... |
| preAssociationProbeFiltering | Filtering probes |
| promoterMeth | promoterMeth to calculate associations of gene expression... |
| render_report | Build report for TCGA.pipe function |
| scatter | scatter |
| scatter.plot | scatter.plot to plot scatter plots between gene expression... |
| schematic.plot | schematic.plot to plot schematic plots showing the locations... |
| Stat.diff.meth | Stat.diff.meth |
| Stat.nonpara | U test (non parameter test) for permutation. This is one... |
| Stat.nonpara.permu | Stat.nonpara.permu |
| summarizeTF | Make MR TF binary table |
| TCGA.pipe | ELMER analysis pipeline for TCGA data. |
| TF.rank.plot | TF.rank.plot to plot the scores (-log10(P value)) which... |
| TFsurvival.plot | Creates survival plot of based on the expression of a TF |
