MEE.data An S4 class contains 5 slots: methylation, expression, sample information, probe information and gene information. MEE.data class are the main input for main functions.
TCGA.pipe
(Package: ELMER) :
ELMER analysis pipeline for TCGA data.
ELMER analysis pipeline for TCGA data. This pipeline combine every steps of ELMER analyses: get.feature.probe, get.diff.meth, get.pair, get.permu, get.enriched.motif and get.TFs. Every steps' results are saved.
TF.rank.plot
(Package: ELMER) :
TF.rank.plot to plot the scores (-log10(P value)) which assess the
TF.rank.plot is a function to plot the scores (-log10(P value)) which assess the correlation between TF expression and average DNA methylation at motif sites. The the motif relevant TF and top3 TFs will be labeled in a different color.
fetch.mee is a funtion to take in DNA methylation, RNA expression, sample information probe information and gene annotation generating a MEE.data class object, which is the input for main functions. Options (meth, exp, sample, probeInfo, geneInfo) can take in R object or read files by specifying file paths. When TCGA is specified, sample information will be automatically generated such as Control/Experiment labels.
fetch.pair is a funtion to take in enhancer-gene linkage prediction information, probe information and gene annotation generating a Pair class object, which is the input for plotting functions. Options (pair, probeInfo, geneInfo) can take in R object or read files by specifying file paths.
get.TFs is a function to identify regulatory TFs based on motif analysis and association analysis between the probes containing a particular motif and expression of all known TFs. If save is ture, two files will be saved: getTF.XX.significant.TFs.with.motif.summary.csv and getTF.hypo.TFs.with.motif.pvalue.rda (see detail).
get.diff.meth applys one-way t-test to identify the CpG sites that are significantly hypo/hyper-methyalated using proportional samples (defined by percentage option) from control and experimental groups. The P values will be adjusted by Benjamini-Hochberg method. Option pvalue and sig.dif will be the criteria (cutoff) for selecting significant differentially methylated CpG sites. If save is TURE, two getMethdiff.XX.csv files will be generated (see detail).
get.enriched.motif is a function make use of Probes.motif data from ELMER.data package to calculate the motif enrichment Odds Ratio and 95% confidence interval for a given set of probes. If save is TURE, two output files will be saved: getMotif.XX.enriched.motifs.rda and getMotif.XX.motif.enrichment.csv (see detail).
providing 
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