DNA IP-seq data analysis

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Documentation for package ‘MEDIPS’ version 1.60.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.

Help Pages

A B C E G M N P R S U W

MEDIPS-package

(MeD)IP-seq data analysis

-- A --

adjustReads

MEDIPSset class and internal functions

-- B --

bin.ROIs	Creates a MEDIPS ROI SET by reading a suitable input file
bin_number	MEDIPSroiSet class and internal functions
bin_number-method	MEDIPSroiSet class and internal functions
bin_size	MEDIPSset class and internal functions
bin_size-method	MEDIPSset class and internal functions

-- C --

chr_lengths	MEDIPSset class and internal functions
chr_lengths-method	COUPLINGset class and internal functions
chr_lengths-method	MEDIPSroiSet class and internal functions
chr_lengths-method	MEDIPSset class and internal functions
chr_names	MEDIPSset class and internal functions
chr_names-method	COUPLINGset class and internal functions
chr_names-method	MEDIPSroiSet class and internal functions
chr_names-method	MEDIPSset class and internal functions
COUPLINGset	COUPLINGset class and internal functions
COUPLINGset-class	COUPLINGset class and internal functions

-- E --

extend	MEDIPSset class and internal functions
extend-method	MEDIPSroiSet class and internal functions
extend-method	MEDIPSset class and internal functions

-- G --

genome_CF	COUPLINGset class and internal functions
genome_CF-method	COUPLINGset class and internal functions
genome_count	MEDIPSset class and internal functions
genome_count-method	MEDIPSroiSet class and internal functions
genome_count-method	MEDIPSset class and internal functions
genome_name	MEDIPSset class and internal functions
genome_name-method	COUPLINGset class and internal functions
genome_name-method	MEDIPSroiSet class and internal functions
genome_name-method	MEDIPSset class and internal functions
getGRange	MEDIPSset class and internal functions
getMObjectFromWIG	Creates a MEDIPS SET by reading a suitable input file
getPairedGRange	Creates a MEDIPS SET by reading a suitable input file
getTypes	MEDIPSset class and internal functions

-- M --

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.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.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.exportWIG	Exports count, rpkm, or sequence pattern densities into a wiggle file.
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.plotCalibrationPlot	Creates the calibration plot.
MEDIPS.plotSaturation	Function plots the results of the MEDIPS.saturationAnalysis function.
MEDIPS.plotSeqCoverage	Function plots the results of the MEDIPS.seqCoverage function.
MEDIPS.rms	MEDIPSset class and internal functions
MEDIPS.saturation	Function calculates the saturation/reproducibility of the provided IP-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.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.
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

-- N --

number_pattern	COUPLINGset class and internal functions
number_pattern-method	COUPLINGset class and internal functions
number_regions	MEDIPSset class and internal functions
number_regions-method	MEDIPSroiSet class and internal functions
number_regions-method	MEDIPSset class and internal functions

-- P --

path_name	MEDIPSset class and internal functions
path_name-method	MEDIPSroiSet class and internal functions
path_name-method	MEDIPSset class and internal functions

-- R --

readRegionsFile	Creates a MEDIPS SET by reading a suitable input file
ROI-method	MEDIPSroiSet class and internal functions
rois	MEDIPSroiSet class and internal functions
rois-method	MEDIPSroiSet class and internal functions

-- S --

sample_name	MEDIPSset class and internal functions
sample_name-method	MEDIPSroiSet class and internal functions
sample_name-method	MEDIPSset class and internal functions
scanBamToGRanges	Creates a MEDIPS SET by reading a suitable input file
seq_pattern	COUPLINGset class and internal functions
seq_pattern-method	COUPLINGset class and internal functions
setTypes	MEDIPSset class and internal functions
shifted	MEDIPSset class and internal functions
shifted-method	MEDIPSroiSet class and internal functions
shifted-method	MEDIPSset class and internal functions
show	MEDIPSset class and internal functions
show-method	COUPLINGset class and internal functions
show-method	MEDIPSroiSet class and internal functions
show-method	MEDIPSset class and internal functions

-- U --

uniq	MEDIPSset class and internal functions
uniq-method	MEDIPSroiSet class and internal functions
uniq-method	MEDIPSset class and internal functions

-- W --

window_size	MEDIPSset class and internal functions
window_size-method	COUPLINGset class and internal functions
window_size-method	MEDIPSset class and internal functions