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...

Functions

fetch.mee Man page
fetch.pair Man page
get450K Man page
getClinic Man page
get.diff.meth Man page
get.enriched.motif Man page
getExp Man page
getExp,MEE.data-method Man page
get.feature.probe Man page
getGeneID Man page
getGeneInfo Man page
getGeneInfo,ANY-method Man page
getMeth Man page
getMeth,MEE.data-method Man page
GetNearGenes Man page
get.pair Man page
getPair Man page
getPair,Pair-method Man page
get.permu Man page
getProbeInfo Man page
getProbeInfo,ANY-method Man page
getRNAseq Man page
getSample Man page
getSample,MEE.data-method Man page
getSymbol Man page
getTCGA Man page
get.TFs Man page
MEE.data-class Man page
motif.enrichment.plot Man page
Pair-class Man page
promoterMeth Man page
scatter.plot Man page
schematic.plot Man page
TCGA.pipe Man page
TF.rank.plot Man page
txs Man page

Files

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

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