DNA IP-seq data analysis


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Documentation for package ‘MEDIPS’ version 1.18.0

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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