MEDIPS-package | (MeD)IP-seq data analysis |
adjustReads | MEDIPSset class and internal functions |
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 |
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 |
extend | MEDIPSset class and internal functions |
extend-method | MEDIPSroiSet class and internal functions |
extend-method | MEDIPSset class and internal functions |
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 |
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 |
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 |
path_name | MEDIPSset class and internal functions |
path_name-method | MEDIPSroiSet class and internal functions |
path_name-method | MEDIPSset class and internal functions |
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 |
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 |
uniq | MEDIPSset class and internal functions |
uniq-method | MEDIPSroiSet class and internal functions |
uniq-method | MEDIPSset class and internal functions |
window_size | MEDIPSset class and internal functions |
window_size-method | COUPLINGset class and internal functions |
window_size-method | MEDIPSset class and internal functions |