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
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
PInter-class            PInter S4 Class
PIntra-class            PIntra S4 Class
PSFit-class             PSFit S4 Class
PSelf-class             PSelf S4 Class
PeaksToGRanges          Convert peaks to GRanges object
PeaksToNarrowPeak       Convert Peaks to narrowPeak (BED) object.
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'
TagsToGInteractions     Convert PETs to GInteractions object
exportPeaks             Exports peaks to csv file
plot                    plot methods for MACPET classes
summary                 summary methods for the MACPET classes.
