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" |