Man pages for FourCSeq
Package analyse 4C sequencing data
| 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... |
| 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 |
| 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... |
| 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' |
