![[R logo]](../../../doc/html/Rlogo.svg)
![[Up]](../../../doc/html/left.jpg)
![[Top]](../../../doc/html/up.jpg)
| fetch.mee | fetch.mee to generate MEE.data class object. |
| fetch.pair | fetch.pair to generate Pair class object. |
| get.diff.meth | get.diff.meth to identify hypo/hyper-methylated CpG sites on HM450K between control and experimental groups such as normal verus tumor samples. |
| 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.TFs | get.TFs to identify regulatory TFs. |
| get450K | get450K to download HM40K DNA methylation data for certain cancer types from TCGA website. |
| getClinic | getClinic to download clinic data for certain cancer types from TCGA website. |
| getExp | getExp to extract RNA expression slot from a MEE.data class object. |
| getExp-method | getExp to extract RNA expression slot from a MEE.data class object. |
| getGeneID | getGeneID to report gene id from symbol |
| getGeneInfo | getGeneInfo to extract geneInfo slot from MEE.data or Pair object. |
| getGeneInfo-method | getGeneInfo to extract geneInfo slot from MEE.data or Pair object. |
| getMeth | getMeth to extract DNA methylation slot from a MEE.data class object. |
| getMeth-method | getMeth to extract DNA methylation slot from a MEE.data class object. |
| GetNearGenes | GetNearGenes to collect nearby genes for one locus. |
| getPair | getPair to extract pairInfo slot from Pair object. |
| getPair-method | getPair to extract pairInfo slot from Pair object. |
| getProbeInfo | getProbeInfo to extract probeInfo slot from MEE.data or Pair object. |
| getProbeInfo-method | getProbeInfo to extract probeInfo slot from MEE.data or Pair object. |
| getRNAseq | getRNAseq to download all RNAseq data for a certain cancer type from TCGA. |
| getSample | getSample to extract sample information from MEE.data object. |
| getSample-method | 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 clinic data for all samples of certain cancer type from TCGA. |
| MEE.data-class | MEE.data An S4 class contains 5 slots: methylation, expression, sample information, probe information and gene information. MEE.data class are the main input for main functions. |
| motif.enrichment.plot | motif.enrichment.plot to plot bar plots showing motif enrichment ORs and 95% confidence interval for ORs |
| Pair-class | An S4 class that pairs information, probe information and gene information. |
| promoterMeth | promoterMeth to calculate associations of gene expression with DNA methylation at promoter regions. |
| 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. |
| 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. |
| txs | txs to fetch USCS gene annotation (transcripts level) from Bioconductor package Homo.sapians. If upstream and downstream are specified in TSS list, promoter regions of USCS gene will be generated. |