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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" |