Man pages for IoannisVardaxis/MACPET
Model based analysis for paired-end data
| AnalysisStatistics | Count Statistics for ChIA-PET. |
| ConvertToPE_BAM | Convert two BAM files into one paired-end BAM file. |
| ConvertToPSelf | Convert GInteraction object to PSelf object |
| exportPeaks | Exports peaks to csv file |
| GenomeMap-class | GenomeMap S4 Class |
| GetShortestPath | Find shortest path between pairs of peaks given a set of... |
| GetSignInteractions | Get the significant interactions of a 'GenomeMap' object |
| MACPET | An R-package for binding site analysis of ChIA-PET data. |
| MACPET_GenomeMapData.rda | Genomic interactions from ChIA-PET data |
| MACPET_pinterData.rda | Inter-chromosomal PETs from ChIA-PET data |
| MACPET_pintraData.rda | Intra-chromosomal PETs from ChIA-PET data |
| MACPET_pselfData.rda | Self-ligated PETs from ChIA-PET data |
| MACPET_psfitData.rda | Self-ligated PETs from ChIA-PET data |
| MACPETUlt | Paired-end Tag (PET) Analysis Function. |
| PeaksToGRanges | Convert peaks to GRanges object |
| PeaksToNarrowPeak | Convert Peaks to narrowPeak (BED) object. |
| PInter-class | PInter S4 Class |
| PIntra-class | PIntra S4 Class |
| plot | plot methods for MACPET classes |
| PSelf-class | PSelf S4 Class |
| PSFit-class | PSFit S4 Class |
| SampleChIAPETData.bam | Subset sample of ChIA-PET data |
| SampleChIAPETDataRead_1.bam | First reads from a subset of ChIA-PET data in... |
| SampleChIAPETDataRead_2.bam | Second reads from a subset of ChIA-PET data in... |
| summary | summary methods for the MACPET classes. |
| TagsToGInteractions | Convert PETs to GInteractions object |
