MACPET-package | An R-package for binding site analysis of ChIA-PET 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 |
ConvertToPSelf.default | Convert GInteraction object to PSelf object |
ConvertToPSelf.GInteractions | Convert GInteraction object to PSelf object |
exportPeaks | Exports peaks to csv file |
exportPeaks.default | Exports peaks to csv file |
exportPeaks.PSFit | Exports peaks to csv file |
MACPET | An R-package for binding site analysis of ChIA-PET data. |
MACPETUlt | Paired-end Tag (PET) Analysis Function. |
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 |
PeaksToGRanges | Convert peaks to GRanges object |
PeaksToGRanges.default | Convert peaks to GRanges object |
PeaksToGRanges.PSFit | Convert peaks to GRanges object |
PeaksToNarrowPeak | Convert Peaks to narrowPeak (BED) object. |
PeaksToNarrowPeak.default | Convert Peaks to narrowPeak (BED) object. |
PeaksToNarrowPeak.PSFit | Convert Peaks to narrowPeak (BED) object. |
PInter | PInter S4 Class |
PInter-class | PInter S4 Class |
PIntra | PIntra S4 Class |
PIntra-class | PIntra S4 Class |
plot | plot methods for MACPET classes |
plot.PInter | plot methods for MACPET classes |
plot.PIntra | plot methods for MACPET classes |
plot.PSelf | plot methods for MACPET classes |
plot.PSFit | plot methods for MACPET classes |
PSelf | PSelf S4 Class |
PSelf-class | PSelf S4 Class |
PSFit | PSFit 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 'SampleChIAPETData.bam' |
SampleChIAPETDataRead_2.bam | Second reads from a subset of ChIA-PET data in 'SampleChIAPETData.bam' |
summary | summary methods for the MACPET classes. |
summary.PInter | summary methods for the MACPET classes. |
summary.PIntra | summary methods for the MACPET classes. |
summary.PSelf | summary methods for the MACPET classes. |
summary.PSFit | summary methods for the MACPET classes. |
TagsToGInteractions | Convert PETs to GInteractions object |
TagsToGInteractions.default | Convert PETs to GInteractions object |
TagsToGInteractions.PSFit | Convert PETs to GInteractions object |