MEDIPS-package	MEDIPS-package
adjustReads	MEDIPSset-class
bin.ROIs	MEDIPS.createROIset
bin_number	MEDIPSroiSet-class
bin_number,MEDIPSroiSet-method	MEDIPSroiSet-class
bin_size	MEDIPSset-class
bin_size,MEDIPSset-method	MEDIPSset-class
chr_lengths	MEDIPSset-class
chr_lengths,COUPLINGset-method	COUPLINGset-class
chr_lengths,MEDIPSroiSet-method	MEDIPSroiSet-class
chr_lengths,MEDIPSset-method	MEDIPSset-class
chr_names	MEDIPSset-class
chr_names,COUPLINGset-method	COUPLINGset-class
chr_names,MEDIPSroiSet-method	MEDIPSroiSet-class
chr_names,MEDIPSset-method	MEDIPSset-class
COUPLINGset	COUPLINGset-class
COUPLINGset-class	COUPLINGset-class
extend	MEDIPSset-class
extend,MEDIPSroiSet-method	MEDIPSroiSet-class
extend,MEDIPSset-method	MEDIPSset-class
genome_CF	COUPLINGset-class
genome_CF,COUPLINGset-method	COUPLINGset-class
genome_count	MEDIPSset-class
genome_count,MEDIPSroiSet-method	MEDIPSroiSet-class
genome_count,MEDIPSset-method	MEDIPSset-class
genome_name	MEDIPSset-class
genome_name,COUPLINGset-method	COUPLINGset-class
genome_name,MEDIPSroiSet-method	MEDIPSroiSet-class
genome_name,MEDIPSset-method	MEDIPSset-class
getGRange	MEDIPSset-class
getMObjectFromWIG	MEDIPS.createSet
getPairedGRange	MEDIPS.createSet
getTypes	MEDIPSset-class
matDiff	MEDIPSset-class
matMax	MEDIPSset-class
matMean	MEDIPSset-class
matMin	MEDIPSset-class
matNnotNA	MEDIPSset-class
matSd	MEDIPSset-class
matTtest	MEDIPSset-class
MEDIPS	MEDIPS-package
MEDIPS.addCNV	MEDIPS.addCNV
MEDIPS.annotate	MEDIPS.annotate
MEDIPS.Bam2GRanges	MEDIPSset-class
MEDIPS.Bed2Granges	MEDIPSset-class
MEDIPS.calibrationCurve	MEDIPSset-class
MEDIPS.cnv	MEDIPSset-class
MEDIPS.correlation	MEDIPS.correlation
MEDIPS.couplingVector	MEDIPS.couplingVector
MEDIPS.coverageAnalysis	MEDIPS.coverageAnalysis
MEDIPS.CpGenrich	MEDIPS.CpGenrich
MEDIPS.createROIset	MEDIPS.createROIset
MEDIPS.createSet	MEDIPS.createSet
MEDIPS.diffMeth	MEDIPS.meth
MEDIPS.distributeReads	MEDIPSset-class
MEDIPS.exportWIG	MEDIPS.exportWIG
MEDIPS.genomeVector	MEDIPS.genomeVector
MEDIPS.GenomicCoordinates	MEDIPSset-class
MEDIPS.getAnnotation	MEDIPS.getAnnotation
MEDIPS.getPositions	MEDIPSset-class
MEDIPS.mergeFrames	MEDIPS.mergeFrames
MEDIPS.mergeSets	MEDIPS.mergeSets
MEDIPS.meth	MEDIPS.meth
MEDIPS.methylProfiling	MEDIPS.methylProfiling
MEDIPS.negBin	MEDIPSset-class
MEDIPS.normalize	MEDIPS.normalize
MEDIPS.plotCalibrationPlot	MEDIPS.plotCalibrationPlot
MEDIPS.plotCoverage	MEDIPS.plotCoverage
MEDIPS.plotSaturation	MEDIPS.plotSaturation
MEDIPS.plotSeqCoverage	MEDIPS.plotSeqCoverage
MEDIPS.pois	MEDIPSset-class
MEDIPS.readAlignedSequences	MEDIPS.readAlignedSequences
MEDIPS.rms	MEDIPSset-class
MEDIPS.saturation	MEDIPS.saturation
MEDIPS.saturationAnalysis	MEDIPS.saturationAnalysis
MEDIPS.selectROIs	MEDIPS.selectROIs
MEDIPS.selectSig	MEDIPS.selectSig
MEDIPS.selectSignificants	MEDIPS.selectSignificants
MEDIPS.seqCoverage	MEDIPS.seqCoverage
MEDIPS.setAnnotation	MEDIPS.setAnnotation
MEDIPS.transform	MEDIPSset-class
MEDIPSroiSet	MEDIPSroiSet-class
MEDIPSroiSet-class	MEDIPSroiSet-class
MEDIPSset	MEDIPSset-class
MEDIPSset-class	MEDIPSset-class
number_pattern	COUPLINGset-class
number_pattern,COUPLINGset-method	COUPLINGset-class
number_regions	MEDIPSset-class
number_regions,MEDIPSroiSet-method	MEDIPSroiSet-class
number_regions,MEDIPSset-method	MEDIPSset-class
path_name	MEDIPSset-class
path_name,MEDIPSroiSet-method	MEDIPSroiSet-class
path_name,MEDIPSset-method	MEDIPSset-class
readRegionsFile	MEDIPS.createSet
ROI,MEDIPSroiSet-method	MEDIPSroiSet-class
rois	MEDIPSroiSet-class
rois,MEDIPSroiSet-method	MEDIPSroiSet-class
sample_name	MEDIPSset-class
sample_name,MEDIPSroiSet-method	MEDIPSroiSet-class
sample_name,MEDIPSset-method	MEDIPSset-class
scanBamToGRanges	MEDIPS.createSet
seq_pattern	COUPLINGset-class
seq_pattern,COUPLINGset-method	COUPLINGset-class
setTypes	MEDIPSset-class
shifted	MEDIPSset-class
shifted,MEDIPSroiSet-method	MEDIPSroiSet-class
shifted,MEDIPSset-method	MEDIPSset-class
show	MEDIPSset-class
show,COUPLINGset-method	COUPLINGset-class
show,MEDIPSroiSet-method	MEDIPSroiSet-class
show,MEDIPSset-method	MEDIPSset-class
uniq	MEDIPSset-class
uniq,MEDIPSroiSet-method	MEDIPSroiSet-class
uniq,MEDIPSset-method	MEDIPSset-class
window_size	MEDIPSset-class
window_size,COUPLINGset-method	COUPLINGset-class
window_size,MEDIPSset-method	MEDIPSset-class
