Inferring Regulatory Element Landscapes and Transcription Factor Networks Using Cancer Methylomes


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Documentation for package ‘ELMER’ version 1.6.0

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.