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MEDIPS (version 1.22.0)

DNA IP-seq data analysis

Description

MEDIPS was developed for analyzing data derived from methylated DNA immunoprecipitation (MeDIP) experiments followed by sequencing (MeDIP-seq). However, MEDIPS provides functionalities for the analysis of any kind of quantitative sequencing data (e.g. ChIP-seq, MBD-seq, CMS-seq and others) including calculation of differential coverage between groups of samples and saturation and correlation analysis.

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Version

Version

1.22.0

License

GPL (>=2)

Maintainer

Lukas Chavez

Last Published

February 15th, 2017

Functions in MEDIPS (1.22.0)

MEDIPS.meth

Funtion summarizes coverage profiles for given MEDIPS SETs and allows to calculate differental coverage and copy number vartiation, if applicable.
MEDIPS.plotSeqCoverage

Function plots the results of the MEDIPS.seqCoverage function.
MEDIPS.correlation

Calculates pairwise Pearson correlations between provided MEDIPS SETs
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-package

(MeD)IP-seq data analysis
MEDIPS.mergeFrames

Merges genomic coordinates of neighboring windows into one supersized window
COUPLINGset-class

COUPLINGset class and internal functions
MEDIPS.getAnnotation

Funtion to fetch annotations from biomaRt.
MEDIPSroiSet-class

MEDIPSroiSet class and internal functions
MEDIPS.plotCalibrationPlot

Creates the calibration plot.
MEDIPS.exportWIG

Exports count, rpkm, or sequence pattern densities into a wiggle file.
MEDIPS.saturation

Function calculates the saturation/reproducibility of the provided IP-Seq data.
MEDIPSset-class

MEDIPSset class and internal functions
MEDIPS.couplingVector

Calculates the sequence pattern densities at genome wide windows.
MEDIPS.createSet

Creates a MEDIPS SET by reading a suitable input file
MEDIPS.plotSaturation

Function plots the results of the MEDIPS.saturationAnalysis function.
MEDIPS.seqCoverage

The function identifies the number of CpGs (or any other predefined sequence pattern) covered by the given short reads.
MEDIPS.addCNV

Function to run a copy number variation analysis.
MEDIPS.setAnnotation

Funtion to annotate a matrix of genomic coordinates (i.e. a result table) by a given annotation object.
MEDIPS.mergeSets

Creates one merged MEDIPS SET out of two.
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