# Model based analysis for paired-end data

## Documentation for package ‘MACPET’ version 1.6.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

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-method | 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-method | Exports peaks to csv file
exportPeaks.default | Exports peaks to csv file
exportPeaks.PSFit | Exports peaks to csv file
GenomeMap | GenomeMap S4 Class
GenomeMap-class | GenomeMap S4 Class
GetShortestPath | Find shortest path between pairs of peaks given a set of significant interactions.
GetShortestPath-method | Find shortest path between pairs of peaks given a set of significant interactions.
GetShortestPath.default | Find shortest path between pairs of peaks given a set of significant interactions.
GetShortestPath.GenomeMap | Find shortest path between pairs of peaks given a set of significant interactions.
GetSignInteractions | Get the significant interactions of a 'GenomeMap' object
GetSignInteractions-method | Get the significant interactions of a 'GenomeMap' object
GetSignInteractions.default | Get the significant interactions of a 'GenomeMap' object
GetSignInteractions.GenomeMap | Get the significant interactions of a 'GenomeMap' object
MACPET | An R-package for binding site analysis of ChIA-PET data.
MACPETUlt | Paired-end Tag (PET) Analysis Function.
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
PeaksToGRanges | Convert peaks to GRanges object
PeaksToGRanges-method | 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-method | 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.GenomeMap | 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-method | summary methods for the MACPET classes.
summary.GenomeMap | 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-method | Convert PETs to GInteractions object
TagsToGInteractions.default | Convert PETs to GInteractions object
TagsToGInteractions.PSFit | Convert PETs to GInteractions object