Man pages for FourCSeq
Package analyse 4C sequencing data

addFragmentsAdd the restriction fragment information
addPeaksAdd peaks based on z-scores and adjusted p-values
addViewpointFragsAdd the information of the viewpoint fragments
combineFragEndsCombine the counts of both fragment ends.
countFragmentOverlapsCount fragment overlaps
countFragmentOverlapsSecondCutterCount fragment overlaps when sequencing was performed from...
distFitMonotoneFit the distance dependency
distFitMonotoneSymmetricFit the distance dependency
fcFourC object with counts
fcfFourC object with z-scores
findViewpointFragmentsFind the fragments to which the viewpoint primers map.
FourCFourC-class
getAllResultsFourCSeq analysis results
getDifferencesDetect differences
getDistAroundVpgetDistAroundVp
getNormalizationFactorsGet normalization factors for each fragment
getReferenceSeqFunction to read reference sequences
getZScoresCalculate z-scores using the residuals of the general trend...
normalizeRPMNormalize count data to rpm
plotDifferencesPlot differences
plotFitsPlot fit results.
plotNormalizationFactorsPlot the estimated normalization factors.
plotScatterplotScatter
plotZScoresPlot z-score results.
smoothCountsSmooth the counts of neighboring fragments
smoothHitPerCentSmooth the hits of neighboring fragments
writeTrackFilesWrite track files of an selected 'assay'
FourCSeq documentation built on Nov. 1, 2018, 3:38 a.m.