# Inferring Regulatory Element Landscapes and Transcription Factor Networks Using Cancer Methylomes

## Documentation for package ‘ELMER’ version 1.1.1

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

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.