# Inferring Regulatory Element Landscapes and Transcription Factor Networks Using Cancer Methylomes

## Documentation for package ‘ELMER’ version 2.4.4

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

ELMER-package | 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.
addDistNearestTSS | Calculate the distance between probe and gene TSS
addMutCol | Adds mutation information to MAE
calculateEnrichement | Calculate motif Erichment
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 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.
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.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
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
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
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