ELMER: Inferring Regulatory Element Landscapes and Transcription Factor Networks Using Cancer Methylomes

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ELMER is designed to use DNA methylation and gene expression from a large number of samples to infere regulatory element landscape and transcription factor network in primary tissue.

Author
Lijing Yao [aut], Ben Berman [aut], Peggy Farnham [aut], Hui Shen [ctb], Peter Laird [ctb], Simon Coetzee [cre, ctb]
Date of publication
None
Maintainer
Simon Coetzee <Simon.Coetzee@cshs.org>
License
GPL-3
Version
1.4.0

View on Bioconductor

Man pages

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...

Files in this package

ELMER/DESCRIPTION
ELMER/NAMESPACE
ELMER/R
ELMER/R/Class.R
ELMER/R/FetchTCGA.R
ELMER/R/GetNearbyGenes.R
ELMER/R/Main_function.R
ELMER/R/Scatter.plot.R
ELMER/R/Schematic.plot.R
ELMER/R/Small.R
ELMER/R/StatisticTest.R
ELMER/R/TCGA_pipe.R
ELMER/R/generic.R
ELMER/R/methodAccess.R
ELMER/R/motif.TF.Plots.R
ELMER/build
ELMER/build/vignette.rds
ELMER/inst
ELMER/inst/doc
ELMER/inst/doc/vignettes.R
ELMER/inst/doc/vignettes.Rnw
ELMER/inst/doc/vignettes.pdf
ELMER/inst/extdata
ELMER/inst/extdata/getTF.hypo.TFs.with.motif.pvalue.rda
ELMER/inst/extdata/mee.example.rda
ELMER/man
ELMER/man/GetNearGenes.Rd
ELMER/man/MEE.data-class.Rd
ELMER/man/Pair-class.Rd
ELMER/man/TCGA.pipe.Rd
ELMER/man/TF.rank.plot.Rd
ELMER/man/fetch.mee.Rd
ELMER/man/fetch.pair.Rd
ELMER/man/get.TFs.Rd
ELMER/man/get.diff.meth.Rd
ELMER/man/get.enriched.motif.Rd
ELMER/man/get.feature.probe.Rd
ELMER/man/get.pair.Rd
ELMER/man/get.permu.Rd
ELMER/man/get450K.Rd
ELMER/man/getClinic.Rd
ELMER/man/getExp.Rd
ELMER/man/getGeneID.Rd
ELMER/man/getGeneInfo.Rd
ELMER/man/getMeth.Rd
ELMER/man/getPair.Rd
ELMER/man/getProbeInfo.Rd
ELMER/man/getRNAseq.Rd
ELMER/man/getSample.Rd
ELMER/man/getSymbol.Rd
ELMER/man/getTCGA.Rd
ELMER/man/motif.enrichment.plot.Rd
ELMER/man/promoterMeth.Rd
ELMER/man/scatter.plot.Rd
ELMER/man/schematic.plot.Rd
ELMER/man/txs.Rd
ELMER/vignettes
ELMER/vignettes/ELMER.example
ELMER/vignettes/ELMER.example/ID255928.schematic.byGene.pdf
ELMER/vignettes/ELMER.example/Result
ELMER/vignettes/ELMER.example/Result/LUSC
ELMER/vignettes/ELMER.example/Result/LUSC/LUSC_RNA_refined.rda
ELMER/vignettes/ELMER.example/Result/LUSC/LUSC_meth_refined.rda
ELMER/vignettes/ELMER.example/Result/LUSC/geneAnnot.rda
ELMER/vignettes/ELMER.example/Result/LUSC/probeInfo_feature_distal.rda
ELMER/vignettes/ELMER.example/TP53.TFrankPlot.pdf
ELMER/vignettes/ELMER.example/TP53_TP63_TP73.byTF.pdf
ELMER/vignettes/ELMER.example/cg19403323.byprobe.pdf
ELMER/vignettes/ELMER.example/cg19403323.schematic.byProbe.pdf
ELMER/vignettes/ELMER.example/cg19403323_SYT14.bypair.pdf
ELMER/vignettes/ELMER.example/hypo.motif.enrichment.pdf
ELMER/vignettes/vignettes.Rnw