| 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 data (Array) |
| 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 in createMAE function |
| ELMER | ELMER (Enhancer Linking by Methylation/Expression Relationships) |
| findMotifRegion | Use Hocomoco motif and homer to identify motifs in a given region |
| get.diff.meth | Identify hypo/hyper-methylated CpG sites between two groups (i.e. normal vs tumor samples, treated vs untreated). |
| get.enriched.motif | get.enriched.motif to identify the overrepresented motifs in a set of probes (HM450K) regions. |
| get.feature.probe | get.feature.probe to select probes within promoter regions or distal regions. |
| get.pair | get.pair to predict enhancer-gene linkages. |
| get.permu | get.permu to generate permutation results for calculation of empirical P values for each enhancer-gene linkage. |
| Get.Pvalue.p | Calculate empirical Pvalue |
| get.tab | summarize MR TF as a binary table with 1 if TF was found in the analysis, 0 if not |
| get.tabs | Creating matrix for MR TF heatmap |
| get.TFs | get.TFs to identify regulatory TFs. |
| get450K | get450K to download HM40K DNA methylation data for certain cancer types from TCGA website. @description get450K is a function to download latest version of HM450K DNA methylation for all samples of certain cancer types from GDC website. |
| getClinic | getClinic to download clinic data for certain cancer types from TCGA website. |
| getExp | Get Gene expression object from MAE |
| getExpSamples | Get Gene expression object samples from MAE |
| 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. |
| getRandomPairs | Get random pairs |
| getRegionNearGenes | Identifies nearest genes to a region |
| getRNAseq | getRNAseq to download all RNAseq data for a certain cancer type from TCGA. |
| getSymbol | getSymbol to report gene symbol from id |
| getTCGA | getTCGA to download DNA methylation, RNA expression and clinic data for all samples of certain cancer type from TCGA. |
| getTF | Get human TF list from the UNiprot database |
| getTFBindingSites | Get MR TF binding regions infered by ELMER |
| getTFtargets | Get TF target genes |
| getTSS | getTSS to fetch GENCODE gene annotation (transcripts level) from Bioconductor package biomaRt If upstream and downstream are specified in TSS list, promoter regions of GENCODE gene will be generated. |
| heatmapGene | Heatmap for correlation between probes DNA methylation and a single gene expression. |
| 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 and DNA methylation. |
| motif.enrichment.plot | motif.enrichment.plot to plot bar plots showing motif enrichment ORs and 95% confidence interval for ORs |
| preAssociationProbeFiltering | Filtering probes |
| promoterMeth | promoterMeth to calculate associations of gene expression with DNA methylation at promoter regions |
| render_report | Build report for TCGA.pipe function |
| scatter | scatter |
| scatter.plot | scatter.plot to plot scatter plots between gene expression and DNA methylation. |
| schematic.plot | schematic.plot to plot schematic plots showing the locations of genes and probes. |
| Stat.diff.meth | Stat.diff.meth |
| Stat.nonpara | U test (non parameter test) for permutation. This is one probe vs nearby gene which is good for computing each probes for nearby genes. |
| 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 assess the correlation between TF expression and average DNA methylation at motif sites. |
| TFsurvival.plot | Creates survival plot of based on the expression of a TF |