MeDIP-Seq data analysis


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Documentation for package ‘MEDIPS’ version 1.8.0

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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"