matDiff |
MEDIPSset class and internal functions |
matMax |
MEDIPSset class and internal functions |
matMean |
MEDIPSset class and internal functions |
matMin |
MEDIPSset class and internal functions |
matNnotNA |
MEDIPSset class and internal functions |
matSd |
MEDIPSset class and internal functions |
matTtest |
MEDIPSset class and internal functions |
MEDIPS |
(MeD)IP-seq data analysis |
MEDIPS.addCNV |
Function to run a copy number variation analysis. |
MEDIPS.annotate |
Funtion to annotate given genomic coordinates. |
MEDIPS.Bam2GRanges |
MEDIPSset class and internal functions |
MEDIPS.Bed2Granges |
MEDIPSset class and internal functions |
MEDIPS.calibrationCurve |
MEDIPSset class and internal functions |
MEDIPS.cnv |
MEDIPSset class and internal functions |
MEDIPS.correlation |
Calculates pairwise Pearson correlations between provided MEDIPS SETs |
MEDIPS.couplingVector |
Calculates the sequence pattern densities at genome wide windows. |
MEDIPS.coverageAnalysis |
The function identifies the number of CpGs (or any other predefined sequence pattern) covered by the given short reads. |
MEDIPS.CpGenrich |
Calculates CpG enrichment of provided short reads compared to the reference genome. |
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.diffMeth |
Funtion summarizes coverage profiles for given MEDIPS SETs and allows to calculate differental coverage and copy number vartiation, if applicable. |
MEDIPS.distributeReads |
MEDIPSset class and internal functions |
MEDIPS.exportWIG |
Exports count, rpkm, or sequence pattern densities into a wiggle file. |
MEDIPS.genomeVector |
Calculates the genome wide short read coverage on a user specified resolution |
MEDIPS.GenomicCoordinates |
MEDIPSset class and internal functions |
MEDIPS.getAnnotation |
Funtion to fetch annotations from biomaRt. |
MEDIPS.getPositions |
MEDIPSset class and internal functions |
MEDIPS.mergeFrames |
Merges genomic coordinates of neighboring windows into one supersized window |
MEDIPS.mergeSets |
Creates one merged MEDIPS SET out of two. |
MEDIPS.meth |
Funtion summarizes coverage profiles for given MEDIPS SETs and allows to calculate differental coverage and copy number vartiation, if applicable. |
MEDIPS.methylProfiling |
Funtion calculates mean methylation values (rpm, rms, ams), ratios, variances, and p-values comparing two MEDIPS SETs for user supplied regions of interests (ROIs) or for genome wide frames. |
MEDIPS.negBin |
MEDIPSset class and internal functions |
MEDIPS.normalize |
Function that normalizes raw signals by local sequence pattern (e.g. CpG) densities. |
MEDIPS.plotCalibrationPlot |
Creates the calibration plot. |
MEDIPS.plotCoverage |
Function plots the results of the MEDIPS.coverageAnalysis function. |
MEDIPS.plotSaturation |
Function plots the results of the MEDIPS.saturationAnalysis function. |
MEDIPS.plotSeqCoverage |
Function plots the results of the MEDIPS.seqCoverage function. |
MEDIPS.pois |
MEDIPSset class and internal functions |
MEDIPS.readAlignedSequences |
Creates a MEDIPS SET by reading a suitable input file |
MEDIPS.rms |
MEDIPSset class and internal functions |
MEDIPS.saturation |
Function calculates the saturation/reproducibility of the provided IP-Seq data. |
MEDIPS.saturationAnalysis |
Function calculates the saturation/reproducibility of the provided MeDIP-Seq data. |
MEDIPS.selectROIs |
Selects row-wise subsets of a result table as returned by the MEDIPS.meth function. |
MEDIPS.selectSig |
Selects windows which show significant differential coverage between two MEDIPS SETs from a resultTable (as returned by the function MEDIPS.meth). |
MEDIPS.selectSignificants |
Selects candidate ROIs that show significant differential methylation between two MEDIPS SETs. |
MEDIPS.seqCoverage |
The function identifies the number of CpGs (or any other predefined sequence pattern) covered by the given short reads. |
MEDIPS.setAnnotation |
Funtion to annotate a matrix of genomic coordinates (i.e. a result table) by a given annotation object. |
MEDIPS.transform |
MEDIPSset class and internal functions |
MEDIPSroiSet |
MEDIPSroiSet class and internal functions |
MEDIPSroiSet-class |
MEDIPSroiSet class and internal functions |
MEDIPSset |
MEDIPSset class and internal functions |
MEDIPSset-class |
MEDIPSset class and internal functions |