Man pages for lijingya/ELMER
Inferring Regulatory Element Landscapes and Transcription Factor Networks Using Cancer Methylomes

fetch.meefetch.mee to generate MEE.data class object.
fetch.pairfetch.pair to generate Pair class object.
get450Kget450K to download HM40K DNA methylation data for certain...
getClinicgetClinic to download clinic data for certain cancer types...
get.diff.methget.diff.meth to identify hypo/hyper-methylated CpG sites on...
get.enriched.motifget.enriched.motif to identify the overrepresented motifs in...
getExpgetExp to extract RNA expression slot from a MEE.data class...
get.feature.probeget.feature.probe to select probes within promoter regions or...
getGeneIDgetGeneID to report gene id from symbol
getGeneInfogetGeneInfo to extract geneInfo slot from MEE.data or Pair...
getMethgetMeth to extract DNA methylation slot from a MEE.data class...
GetNearGenesGetNearGenes to collect nearby genes for one locus.
get.pairget.pair to predict enhancer-gene linkages.
getPairgetPair to extract pairInfo slot from Pair object.
get.permuget.permu to generate permutation results for calculation of...
getProbeInfogetProbeInfo to extract probeInfo slot from MEE.data or Pair...
getRNAseqgetRNAseq to download all RNAseq data for a certain cancer...
getSamplegetSample to extract sample information from MEE.data object.
getSymbolgetSymbol to report gene symbol from id
getTCGAgetTCGA to download DNA methylation, RNA expression and...
get.TFsget.TFs to identify regulatory TFs.
MEE.data-classMEE.data An S4 class contains 5 slots: methylation,...
motif.enrichment.plotmotif.enrichment.plot to plot bar plots showing motif...
Pair-classAn S4 class that pairs information, probe information and...
promoterMethpromoterMeth to calculate associations of gene expression...
scatter.plotscatter.plot to plot scatter plots between gene expression...
schematic.plotschematic.plot to plot schematic plots showing the locations...
TCGA.pipeELMER analysis pipeline for TCGA data.
TF.rank.plotTF.rank.plot to plot the scores (-log10(P value)) which...
txstxs to fetch USCS gene annotation (transcripts level) from...
lijingya/ELMER documentation built on May 21, 2017, 1:35 p.m.