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FourC-class
● Data Source:
BioConductor
● Keywords: package
● Alias: FourC, FourC-class, updateObject,FourC-method
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addFragments
(Package: FourCSeq) :
Add the restriction fragment information
addFragments adds the genomic position and information of the restriction fragments as GRanges object to rowRanges of the FourC object.
● Data Source:
BioConductor
● Keywords:
● Alias: addFragments
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addPeaks
(Package: FourCSeq) :
Add peaks based on z-scores and adjusted p-values
Fragments are annotated to be a z-score peak (TRUE or FALSE) based on z-scores and fdr values for the given fragment
● Data Source:
BioConductor
● Keywords:
● Alias: addPeaks
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addViewpointFrags
(Package: FourCSeq) :
Add the information of the viewpoint fragments
addViewpointFrags adds the genomic position and information of the viewpoint primer fragments to colData of the FourC object.
● Data Source:
BioConductor
● Keywords:
● Alias: addViewpointFrags
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combineFragEnds
(Package: FourCSeq) :
Combine the counts of both fragment ends.
combineFragEnds combines the counts of both fragment ends. A multiplication factor can be used for fragments that only have counts for one valid fragment end.
● Data Source:
BioConductor
● Keywords:
● Alias: combineFragEnds
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countFragmentOverlaps counts the number of reads mapping to each fragment end in rowRanges of the FourC object.
● Data Source:
BioConductor
● Keywords:
● Alias: countFragmentOverlaps
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countFragmentOverlapsSecondCutter
(Package: FourCSeq) :
Count fragment overlaps when sequencing was performed from the second
countFragmentOverlapsSecondCutter counts the number of reads mapping to each cutting site of the second cutter and then summarizes them over the fragment ends of the first cutter stored in rowRanges of the FourC object.
● Data Source:
BioConductor
● Keywords:
● Alias: countFragmentOverlapsSecondCutter
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distFitMonotone takes the variance stabilized count values and calculates a monotone fit for the distance dependency. The position information about the viewpoint is stored in fragData. The signal trend is fitted for the data left and right to the viewpoint separately using the fda package.
● Data Source:
BioConductor
● Keywords:
● Alias: distFitMonotone
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distFitMonotoneSymmetric takes the variance stabilized count values and calculates a symmetric monotone fit for the distance dependency. The position information about the viewpoint is stored in fragData. The signal trend is fitted for the combined data left and right to the viewpoint using the fda package.
● Data Source:
BioConductor
● Keywords:
● Alias: distFitMonotoneSymmetric
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findViewpointFragments
(Package: FourCSeq) :
Find the fragments to which the viewpoint primers map.
findViewpointFragments finds the position of the viewpoint primer in the reference genome and on which restriction fragment they fall. It saves the results in these files: - projectPath/fragmentDir/primerFragments.rda - projectPath/fragmentDir/primerFragments.txt
● Data Source:
BioConductor
● Keywords:
● Alias: findViewpointFragments
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providing 
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