Package analyse 4C sequencing data


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Documentation for package ‘FourCSeq’ version 1.18.0

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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'