| fetch.mee | fetch.mee to generate MEE.data class object. |
| fetch.pair | fetch.pair to generate Pair class object. |
| get450K | get450K to download HM40K DNA methylation data for certain... |
| getClinic | getClinic to download clinic data for certain cancer types... |
| get.diff.meth | get.diff.meth to identify hypo/hyper-methylated CpG sites on... |
| get.enriched.motif | get.enriched.motif to identify the overrepresented motifs in... |
| getExp | getExp to extract RNA expression slot from a MEE.data class... |
| get.feature.probe | get.feature.probe to select probes within promoter regions or... |
| getGeneID | getGeneID to report gene id from symbol |
| getGeneInfo | getGeneInfo to extract geneInfo slot from MEE.data or Pair... |
| getMeth | getMeth to extract DNA methylation slot from a MEE.data class... |
| GetNearGenes | GetNearGenes to collect nearby genes for one locus. |
| get.pair | get.pair to predict enhancer-gene linkages. |
| getPair | getPair to extract pairInfo slot from Pair object. |
| get.permu | get.permu to generate permutation results for calculation of... |
| getProbeInfo | getProbeInfo to extract probeInfo slot from MEE.data or Pair... |
| getRNAseq | getRNAseq to download all RNAseq data for a certain cancer... |
| getSample | getSample to extract sample information from MEE.data object. |
| getSymbol | getSymbol to report gene symbol from id |
| getTCGA | getTCGA to download DNA methylation, RNA expression and... |
| get.TFs | get.TFs to identify regulatory TFs. |
| MEE.data-class | MEE.data An S4 class contains 5 slots: methylation,... |
| motif.enrichment.plot | motif.enrichment.plot to plot bar plots showing motif... |
| Pair-class | An S4 class that pairs information, probe information and... |
| promoterMeth | promoterMeth to calculate associations of gene expression... |
| scatter.plot | scatter.plot to plot scatter plots between gene expression... |
| schematic.plot | schematic.plot to plot schematic plots showing the locations... |
| TCGA.pipe | ELMER analysis pipeline for TCGA data. |
| TF.rank.plot | TF.rank.plot to plot the scores (-log10(P value)) which... |
| txs | txs to fetch USCS gene annotation (transcripts level) from... |
