Man pages for paolopavan/medips
DNA IP-seq data analysis
| COUPLINGset-class | COUPLINGset class and internal functions |
| MEDIPS.addCNV | Function to run a copy number variation analysis. |
| MEDIPS.correlation | Calculates pairwise Pearson correlations between provided... |
| MEDIPS.couplingVector | Calculates the sequence pattern densities at genome wide... |
| MEDIPS.CpGenrich | Calculates CpG enrichment of provided short reads compared to... |
| MEDIPS.createROIset | Creates a MEDIPS ROI SET by reading a suitable input file |
| MEDIPS.createSet | Creates a MEDIPS SET by reading a suitable input file |
| MEDIPS.exportWIG | Exports count, rpkm, or sequence pattern densities into a... |
| MEDIPS.getAnnotation | Funtion to fetch annotations from biomaRt. |
| MEDIPS.mergeFrames | Merges genomic coordinates of neighboring windows into one... |
| MEDIPS.mergeSets | Creates one merged MEDIPS SET out of two. |
| MEDIPS.meth | Funtion summarizes coverage profiles for given MEDIPS SETs... |
| MEDIPS-package | (MeD)IP-seq data analysis |
| MEDIPS.plotCalibrationPlot | Creates the calibration plot. |
| MEDIPS.plotSaturation | Function plots the results of the MEDIPS.saturationAnalysis... |
| MEDIPS.plotSeqCoverage | Function plots the results of the MEDIPS.seqCoverage... |
| MEDIPSroiSet-class | MEDIPSroiSet class and internal functions |
| MEDIPS.saturation | Function calculates the saturation/reproducibility of the... |
| MEDIPS.selectROIs | Selects row-wise subsets of a result table as returned by the... |
| MEDIPS.selectSig | Selects windows which show significant differential coverage... |
| MEDIPS.seqCoverage | The function identifies the number of CpGs (or any other... |
| MEDIPS.setAnnotation | Funtion to annotate a matrix of genomic coordinates (i.e. a... |
| MEDIPSset-class | MEDIPSset class and internal functions |
