Inferring Regulatory Element Landscapes and Transcription Factor Networks Using Cancer Methylomes


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Documentation for package ‘ELMER’ version 2.16.0

Help Pages

addDistNearestTSS Calculate the distance between probe and gene TSS
addMutCol Adds mutation information to MAE
calcDistNearestTSS Calculate distance from region to nearest TSS
calculateEnrichement Calculate motif Erichment
createBigWigDNAmetArray Create a bigwig file for IGV visualization of DNA methylation data (Array)
createIGVtrack Create a junction track for IGV visualization of interection
createMAE Construct a Multi Assay Experiment for ELMER analysis
createMotifRelevantTfs Get family of transcription factors
createSummaryDocument Create summary document for TCGA.pipe function
createTSVTemplates Create examples files for Sample mapping and information used in createMAE function
ELMER ELMER (Enhancer Linking by Methylation/Expression Relationships)
findMotifRegion Use Hocomoco motif and homer to identify motifs in a given region
get.diff.meth Identify hypo/hyper-methylated CpG sites between two groups (i.e. normal vs tumor samples, treated vs untreated).
get.enriched.motif get.enriched.motif to identify the overrepresented motifs in a set of probes (HM450K) regions.
get.feature.probe get.feature.probe to select probes within promoter regions or distal regions.
get.pair get.pair to predict enhancer-gene linkages.
get.permu get.permu to generate permutation results for calculation of empirical P values for each enhancer-gene linkage.
Get.Pvalue.p Calculate empirical Pvalue
get.tab summarize MR TF as a binary table with 1 if TF was found in the analysis, 0 if not
get.tabs Creating matrix for MR TF heatmap
get.TFs get.TFs to identify regulatory TFs.
get450K get450K to download HM40K DNA methylation data for certain cancer types from TCGA website. @description get450K is a function to download latest version of HM450K DNA methylation for all samples of certain cancer types from GDC website.
getClinic getClinic to download clinic data for certain cancer types from TCGA website.
getExp Get Gene expression object from MAE
getExpSamples Get Gene expression object samples from MAE
getGeneID getGeneID to report gene id from symbol
getMet Get DNA methylation object from MAE
getMetSamples Get DNA methylation object samples from MAE
GetNearGenes GetNearGenes to collect nearby genes for one locus.
getRandomPairs Get random pairs
getRegionNearGenes Identifies nearest genes to a region
getRNAseq getRNAseq to download all RNAseq data for a certain cancer type from TCGA.
getSymbol getSymbol to report gene symbol from id
getTCGA getTCGA to download DNA methylation, RNA expression and clinic data for all samples of certain cancer type from TCGA.
getTF Get human TF list from the UNiprot database
getTFBindingSites Get MR TF binding regions infered by ELMER
getTFtargets Get TF target genes
getTSS getTSS to fetch GENCODE gene annotation (transcripts level) from Bioconductor package biomaRt If upstream and downstream are specified in TSS list, promoter regions of GENCODE gene will be generated.
heatmapGene Heatmap for correlation between probes DNA methylation and a single gene expression.
heatmapPairs Heatmap of pairs gene and probes anti-correlated
lm_eqn lable linear regression formula
metBoxPlot scatter.plot to plot scatter plots between gene expression and DNA methylation.
motif.enrichment.plot motif.enrichment.plot to plot bar plots showing motif enrichment ORs and 95% confidence interval for ORs
preAssociationProbeFiltering Filtering probes
promoterMeth promoterMeth to calculate associations of gene expression with DNA methylation at promoter regions
render_report Build report for TCGA.pipe function
scatter scatter
scatter.plot scatter.plot to plot scatter plots between gene expression and DNA methylation.
schematic.plot schematic.plot to plot schematic plots showing the locations of genes and probes.
Stat.diff.meth Stat.diff.meth
Stat.nonpara U test (non parameter test) for permutation. This is one probe vs nearby gene which is good for computing each probes for nearby genes.
Stat.nonpara.permu Stat.nonpara.permu
summarizeTF Make MR TF binary table
TCGA.pipe ELMER analysis pipeline for TCGA data.
TF.rank.plot TF.rank.plot to plot the scores (-log10(P value)) which assess the correlation between TF expression and average DNA methylation at motif sites.
TFsurvival.plot Creates survival plot of based on the expression of a TF