Package analyse 4C sequencing data

Documentation for package ‘FourCSeq’ version 1.4.0

addFragments	Add the restriction fragment information
addPeaks	Add peaks based on z-scores and adjusted p-values
addViewpointFrags	Add the information of the viewpoint fragments
combineFragEnds	Combine the counts of both fragment ends.
countFragmentOverlaps	Count fragment overlaps
countFragmentOverlapsSecondCutter	Count fragment overlaps when sequencing was performed from the second cutting site
distFitMonotone	Fit the distance dependency
distFitMonotoneSymmetric	Fit the distance dependency
fc	FourC object with counts
fcf	FourC object with z-scores
findViewpointFragments	Find the fragments to which the viewpoint primers map.
FourC	FourC-class
FourC-class	FourC-class
getAllResults	FourCSeq analysis results
getDifferences	Detect differences
getDistAroundVp	getDistAroundVp
getNormalizationFactors	Get normalization factors for each fragment
getReferenceSeq	Function to read reference sequences
getZScores	Calculate z-scores using the residuals of the general trend fit.
normalizeRPM	Normalize count data to rpm
plotDifferences	Plot differences
plotFits	Plot fit results.
plotNormalizationFactors	Plot the estimated normalization factors.
plotScatter	plotScatter
plotZScores	Plot z-score results.
smoothCounts	Smooth the counts of neighboring fragments
smoothHitPerCent	Smooth the hits of neighboring fragments
updateObject-method	FourC-class
writeTrackFiles	Write track files of an selected 'assay'