ELMER: Inferring Regulatory Element Landscapes and Transcription Factor Networks Using Cancer Methylomes
Version 1.6.0

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.

Browse man pages Browse package API and functions Browse package files

AuthorLijing Yao [aut], Ben Berman [aut], Peggy Farnham [aut], Hui Shen [ctb], Peter Laird [ctb], Simon Coetzee [cre, ctb]
Bioconductor views DNAMethylation GeneExpression GeneRegulation MotifAnnotation Software
Date of publicationNone
MaintainerSimon Coetzee <Simon.Coetzee@cshs.org>
LicenseGPL-3
Version1.6.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("ELMER")

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

Binary Source code
GeneIDName Source code
Get.Pvalue.p Source code
GetNearGenes Man page Source code
MEE.data-class Man page
NearGenes Source code
Pair-class Man page
Stat.diff.meth Source code
Stat.nonpara Source code
Stat.nonpara.permu Source code
TCGA.pipe Man page Source code
TF.rank.plot Man page Source code
fetch.mee Man page Source code
fetch.pair Man page Source code
get.TFs Man page Source code
get.diff.meth Man page Source code
get.enriched.motif Man page Source code
get.feature.probe Man page Source code
get.pair Man page Source code
get.permu Man page Source code
get450K Man page Source code
getClinic Man page Source code
getExp Man page
getExp,MEE.data-method Man page
getGeneID Man page Source code
getGeneInfo Man page
getGeneInfo,ANY-method Man page
getMeth Man page
getMeth,MEE.data-method Man page
getPair Man page
getPair,Pair-method Man page
getProbeInfo Man page
getProbeInfo,ANY-method Man page
getRNAseq Man page Source code
getSample Man page
getSample,MEE.data-method Man page
getSymbol Man page Source code
getTCGA Man page Source code
lm_eqn Source code
matrixClinic Source code
matrixMeth Source code
matrixRNA Source code
mee.data Source code
motif.enrichment.plot Man page Source code
pair.data Source code
promoterMeth Man page Source code
scatter Source code
scatter.plot Man page Source code
schematic Source code
schematic.plot Man page Source code
splitmatrix Source code
standardizeTcgaId Source code
tcgaSampleType Source code
txs Man page Source code

Files

DESCRIPTION
NAMESPACE
R
R/Class.R
R/FetchTCGA.R
R/GetNearbyGenes.R
R/Main_function.R
R/Scatter.plot.R
R/Schematic.plot.R
R/Small.R
R/StatisticTest.R
R/TCGA_pipe.R
R/generic.R
R/methodAccess.R
R/motif.TF.Plots.R
build
build/vignette.rds
inst
inst/doc
inst/doc/vignettes.R
inst/doc/vignettes.Rnw
inst/doc/vignettes.pdf
inst/extdata
inst/extdata/getTF.hypo.TFs.with.motif.pvalue.rda
inst/extdata/mee.example.rda
man
man/GetNearGenes.Rd
man/MEE.data-class.Rd
man/Pair-class.Rd
man/TCGA.pipe.Rd
man/TF.rank.plot.Rd
man/fetch.mee.Rd
man/fetch.pair.Rd
man/get.TFs.Rd
man/get.diff.meth.Rd
man/get.enriched.motif.Rd
man/get.feature.probe.Rd
man/get.pair.Rd
man/get.permu.Rd
man/get450K.Rd
man/getClinic.Rd
man/getExp.Rd
man/getGeneID.Rd
man/getGeneInfo.Rd
man/getMeth.Rd
man/getPair.Rd
man/getProbeInfo.Rd
man/getRNAseq.Rd
man/getSample.Rd
man/getSymbol.Rd
man/getTCGA.Rd
man/motif.enrichment.plot.Rd
man/promoterMeth.Rd
man/scatter.plot.Rd
man/schematic.plot.Rd
man/txs.Rd
vignettes
vignettes/vignettes.Rnw
ELMER documentation built on May 20, 2017, 10:38 p.m.