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

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.

AuthorLijing Yao [aut], Ben Berman [aut], Peggy Farnham [aut], Hui Shen [ctb], Peter Laird [ctb], Simon Coetzee [cre, ctb]
Date of publicationNone
MaintainerSimon Coetzee <Simon.Coetzee@cshs.org>
LicenseGPL-3
Version1.4.0

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

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