Man pages for MEDIPS
DNA IP-seq data analysis

COUPLINGset-classCOUPLINGset class and internal functions
MEDIPS.addCNVFunction to run a copy number variation analysis.
MEDIPS.correlationCalculates pairwise Pearson correlations between provided...
MEDIPS.couplingVectorCalculates the sequence pattern densities at genome wide...
MEDIPS.CpGenrichCalculates CpG enrichment of provided short reads compared to...
MEDIPS.createROIsetCreates a MEDIPS ROI SET by reading a suitable input file
MEDIPS.createSetCreates a MEDIPS SET by reading a suitable input file
MEDIPS.exportWIGExports count, rpkm, or sequence pattern densities into a...
MEDIPS.getAnnotationFuntion to fetch annotations from biomaRt.
MEDIPS.mergeFramesMerges genomic coordinates of neighboring windows into one...
MEDIPS.mergeSetsCreates one merged MEDIPS SET out of two.
MEDIPS.methFuntion summarizes coverage profiles for given MEDIPS SETs...
MEDIPS-package(MeD)IP-seq data analysis
MEDIPS.plotCalibrationPlotCreates the calibration plot.
MEDIPS.plotSaturationFunction plots the results of the MEDIPS.saturationAnalysis...
MEDIPS.plotSeqCoverageFunction plots the results of the MEDIPS.seqCoverage...
MEDIPSroiSet-classMEDIPSroiSet class and internal functions
MEDIPS.saturationFunction calculates the saturation/reproducibility of the...
MEDIPS.selectROIsSelects row-wise subsets of a result table as returned by the...
MEDIPS.selectSigSelects windows which show significant differential coverage...
MEDIPS.seqCoverageThe function identifies the number of CpGs (or any other...
MEDIPS.setAnnotationFuntion to annotate a matrix of genomic coordinates (i.e. a...
MEDIPSset-classMEDIPSset class and internal functions
MEDIPS documentation built on Nov. 1, 2018, 3:38 a.m.