# MeDIP-Seq data analysis

## Documentation for package ‘MEDIPS’ version 1.2.0

- DESCRIPTION file.
- Overview of user guides and package vignettes; browse directory.

## Help Pages

MEDIPS-package | MeDIP-Seq data analysis
bin_size | Class "MEDIPSset"
bin_size-method | Class "MEDIPSset"
calcurve_mean_coupling | Class "MEDIPSset"
calcurve_mean_coupling-method | Class "MEDIPSset"
calcurve_mean_signals | Class "MEDIPSset"
calcurve_mean_signals-method | Class "MEDIPSset"
calcurve_var | Class "MEDIPSset"
calcurve_var-method | Class "MEDIPSset"
cali_chr | Class "MEDIPSset"
cali_chr-method | Class "MEDIPSset"
chr_lengths | Class "MEDIPSset"
chr_lengths-method | Class "MEDIPSset"
chr_names | Class "MEDIPSset"
chr_names-method | Class "MEDIPSset"
distFile | Class "MEDIPSset"
distFile-method | Class "MEDIPSset"
distFunction | Class "MEDIPSset"
distFunction-method | Class "MEDIPSset"
extend | Class "MEDIPSset"
extend-method | Class "MEDIPSset"
fragmentLength | Class "MEDIPSset"
fragmentLength-method | Class "MEDIPSset"
genome_CF | Class "MEDIPSset"
genome_CF-method | Class "MEDIPSset"
genome_chr | Class "MEDIPSset"
genome_chr-method | Class "MEDIPSset"
genome_name | Class "MEDIPSset"
genome_name-method | Class "MEDIPSset"
genome_norm | Class "MEDIPSset"
genome_norm-method | Class "MEDIPSset"
genome_pos | Class "MEDIPSset"
genome_pos-method | Class "MEDIPSset"
genome_raw | Class "MEDIPSset"
genome_raw-method | Class "MEDIPSset"
intercept | Class "MEDIPSset"
intercept-method | Class "MEDIPSset"
MEDIPS | MeDIP-Seq data analysis
MEDIPS.annotate | Funtion to annotate given genomic coordinates.
MEDIPS.calibrationCurve | Function that calculates the calibration curve
MEDIPS.couplingVector | Calculates the sequence pattern densities for genome wide bins.
MEDIPS.coverageAnalysis | The function identifies the number of CpGs (or any other predefined sequence pattern) covered by the given short reads.
MEDIPS.CpGenrich | Calculates the enrichment of provided CpG rich regions compared to the reference genome.
MEDIPS.distributeReads | Class "MEDIPSset"
MEDIPS.exportWIG | Exports reads per million, relative methylation score or sequence pattern density into a wiggle file.
MEDIPS.genomeVector | Calculates the genome wide short read coverage on a user specified resolution
MEDIPS.getPositions | Identifies genomic sequence pattern positions within the reference genome.
MEDIPS.mergeFrames | Merges genomic coordinates of overlapping frames into one supersized frame
MEDIPS.methylProfiling | Funtion calculates mean methylation values (rpm, rms) and ams values, ratios, variances, and pvalues comparing two MEDIPS SETs for user supplied regions of interests (ROIs) or genome wide frames.
MEDIPS.normalize | Function that normalizes raw signals by local sequence pattern (e.g. CpG) densities.
MEDIPS.plotCalibrationPlot | Plots the results of the MEDIPS.calibrationCurve function.
MEDIPS.plotCoverage | Function plots the results of the MEDIPS.coverageAnalysis function.
MEDIPS.plotSaturation | Function plots the results of the MEDIPS.saturationAnalysis function.
MEDIPS.readAlignedSequences | Creates a MEDIPS SET by reading a suitable input file
MEDIPS.saturationAnalysis | Function calculates the saturation/reproducibility of the provided MeDIP-Seq data.
MEDIPS.selectSignificants | Selects candidate ROIs that show significant differential methylation between two MEDIPS SETs.
MEDIPS.transform | Class "MEDIPSset"
MEDIPSset-class | Class "MEDIPSset"
number_pattern | Class "MEDIPSset"
number_pattern-method | Class "MEDIPSset"
number_regions | Class "MEDIPSset"
number_regions-method | Class "MEDIPSset"
pattern_chr | Class "MEDIPSset"
pattern_chr-method | Class "MEDIPSset"
pattern_pos | Class "MEDIPSset"
pattern_pos-method | Class "MEDIPSset"
regions_chr | Class "MEDIPSset"
regions_chr-method | Class "MEDIPSset"
regions_start | Class "MEDIPSset"
regions_start-method | Class "MEDIPSset"
regions_stop | Class "MEDIPSset"
regions_stop-method | Class "MEDIPSset"
regions_strand | Class "MEDIPSset"
regions_strand-method | Class "MEDIPSset"
sample_name | Class "MEDIPSset"
sample_name-method | Class "MEDIPSset"
seq_pattern | Class "MEDIPSset"
seq_pattern-method | Class "MEDIPSset"
show | Class "MEDIPSset"
show-method | Class "MEDIPSset"
slope | Class "MEDIPSset"
slope-method | Class "MEDIPSset"