# Package analyse 4C sequencing data

## Documentation for package ‘FourCSeq’ version 1.2.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

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
writeTrackFiles | Write track files of an selected 'assay'