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

addDistNearestTSSCalculate the distance between probe and gene TSS
addMutColAdds mutation information to MAE
createMAEConstruct a Multi Assay Experiment for ELMER analysis
createMotifRelevantTfsGet family of transcription factors
createSummaryDocumentCreate summary document for TCGA.pipe function
createTSVTemplatesCreate examples files for Sample mapping and information used...
ELMERELMER is designed to use DNA methylation and gene expression...
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...
getExpGet Gene expression object from MAE
getExpSamplesGet Gene expression object samples from MAE
get.feature.probeget.feature.probe to select probes within promoter regions or...
getGeneIDgetGeneID to report gene id from symbol
getMetGet DNA methylation object from MAE
getMetSamplesGet DNA methylation object samples from MAE
GetNearGenesGetNearGenes to collect nearby genes for one locus.
get.pairget.pair to predict enhancer-gene linkages.
get.permuget.permu to generate permutation results for calculation of...
Get.Pvalue.pCalculate empirical Pvalue
getRNAseqgetRNAseq to download all RNAseq data for a certain cancer...
getSymbolgetSymbol to report gene symbol from id
getTCGAgetTCGA to download DNA methylation, RNA expression and...
getTFGet human TF list from the UNiprot database
get.TFsget.TFs to identify regulatory TFs.
getTSSgetTSS to fetch GENCODE gene annotation (transcripts level)...
heatmapPairsHeatmap of pairs gene and probes anti-correlated
lm_eqnlable linear regression formula
metBoxPlotscatter.plot to plot scatter plots between gene expression...
motif.enrichment.plotmotif.enrichment.plot to plot bar plots showing motif...
preAssociationProbeFilteringFiltering probes
promoterMethpromoterMeth to calculate associations of gene expression...
scatterscatter
scatter.plotscatter.plot to plot scatter plots between gene expression...
schematic.plotschematic.plot to plot schematic plots showing the locations...
Stat.diff.methStat.diff.meth
Stat.nonparaU test (non parameter test) for permutation. This is one...
Stat.nonpara.permuStat.nonpara.permu
TCGA.pipeELMER analysis pipeline for TCGA data.
TF.rank.plotTF.rank.plot to plot the scores (-log10(P value)) which...
TFsurvival.plotCreates survival plot of based on the expression of a TF
ELMER documentation built on Dec. 9, 2017, 2:01 a.m.