Man pages for andigoni/MeinteR
A framework to prioritize DNA methylation aberrations based on conformational and cis-regulatory element enrichment

bed2SeqFetch sequences from bed-formatted data frames
cpgIslandsCpG islands (reference data)
cTFConserved transcription factors (reference data)
filterByCGIFilter by CpG islands
filterByPromFilter by promoters
findAltSplicingFind alternative splicing events
findConservedTFBSFind differentially methylated sites overlapping...
findPalsFind palindromes in a bed-formatted dataset
findQuadsFind quadruplexes in sequences centered at CpG sites
findShapesFind putative conformational DNA changes
findSpliceSitesFind splice sites
findTFBSFind putative transcription factor binding sites
importGEOImport GEO data series in the workspace
importLimmaImports the results of differential methylation analyses...
isEmptyDFCheck if data frame is empty
loadFileLoad input data
loadSeqGEOReformat methylation sequencing data fetched from GEO
meinterCalculate the genomic index of methylation sites based on the...
nameStudySet a study name
plotBetaPlot scores of the input data Generates a density plot of the...
plotCpGPlot G+C-content and observed/expected ratio.
plotTFCreate barplot of the identified transcription factor binding...
refFreqHuman transcription factor frequency (reference data)
reorderBedReorder tabular methylation data to bed format
sampleSample DNA methylation dataset (sample data)
scatterConsTFCreate a scatterplot of the identified conserved...
test.dataTest dataset with chromosomal position of the methylated...
TF.classTranscription factor classes (reference data)
validateBedValidate format of the input bed data
andigoni/MeinteR documentation built on Sept. 16, 2019, 6:24 p.m.