COUPLINGset class and internal functions
(MeD)IP-seq data analysis
Calculates CpG enrichment of provided short reads compared to the reference genome.
Function to run a copy number variation analysis.
Calculates pairwise Pearson correlations between provided MEDIPS SETs
Calculates the sequence pattern densities at genome wide windows.
Creates a MEDIPS ROI SET by reading a suitable input file
Creates a MEDIPS SET by reading a suitable input file
Exports count, rpkm, or sequence pattern densities into a wiggle file.
Funtion to fetch annotations from biomaRt.
Merges genomic coordinates of neighboring windows into one supersized window
Creates one merged MEDIPS SET out of two.
Funtion summarizes coverage profiles for given MEDIPS SETs and allows to calculate differental coverage and copy number vartiation, if applicable.
Creates the calibration plot.
Function plots the results of the MEDIPS.saturationAnalysis function.
Function plots the results of the MEDIPS.seqCoverage function.
Function calculates the saturation/reproducibility of the provided IP-Seq data.
Selects row-wise subsets of a result table as returned by the MEDIPS.meth function.
Selects windows which show significant differential coverage between two MEDIPS SETs from a resultTable (as returned by the function MEDIPS.meth).
The function identifies the number of CpGs (or any other predefined sequence pattern) covered by the given short reads.
Funtion to annotate a matrix of genomic coordinates (i.e. a result table) by a given annotation object.
MEDIPSroiSet class and internal functions
MEDIPSset class and internal functions