Model based analysis for paired-end data


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Documentation for package ‘MACPET’ version 1.0.0

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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