Scale4C: an R/Bioconductor package for scale-space transformation of 4C-seq data

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Documentation for package ‘Scale4C’ version 1.24.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

addPointsOfInterest	Add points of interest to a 'Scale4C' object
addPointsOfInterest-method	Add points of interest to a 'Scale4C' object
calculateFingerprintMap	Calculate scale-space fingerprint map for given 4C-seq data
calculateFingerprintMap-method	Calculate scale-space fingerprint map for given 4C-seq data
calculateScaleSpace	Calculate scale-space representation for given 4C-seq data
calculateScaleSpace-method	Calculate scale-space representation for given 4C-seq data
findSingularities	Find singularities in a provided scale-space fingerprint map
findSingularities-method	Find singularities in a provided scale-space fingerprint map
importBasic4CseqData	Import raw data from a provided Basic4Cseq output file
importBasic4CseqData-method	Import raw data from a provided Basic4Cseq output file
liverData	Example 4C-seq data set of fetal liver data
liverDataVP	Example 4C-seq data set of fetal liver data, with added VP
outputScaleSpaceTree	Output list of all features for a given scale-space map
outputScaleSpaceTree-method	Output list of all features for a given scale-space map
plotInflectionPoints	Draw a smoothed near-cis profile with marked inflection points for a 4C-seq signal
plotInflectionPoints-method	Draw a smoothed near-cis profile with marked inflection points for a 4C-seq signal
plotTesselation	Draw the final scale space tesselation
plotTesselation-method	Draw the final scale space tesselation
plotTraceback	Draw the traceback results for a list of singular points on a fingerprint map
plotTraceback-method	Draw the traceback results for a list of singular points on a fingerprint map
pointsOfInterest	Class '"Scale4C"'
pointsOfInterest-method	Class '"Scale4C"'
pointsOfInterest<-	Class '"Scale4C"'
pointsOfInterest<--method	Class '"Scale4C"'
rawData	Class '"Scale4C"'
rawData-method	Class '"Scale4C"'
rawData<-	Class '"Scale4C"'
rawData<--method	Class '"Scale4C"'
Scale4C	Creating a Scale4C object
Scale4C-class	Class '"Scale4C"'
Scale4C-method	Creating a Scale4C object
scaleSpace	Class '"Scale4C"'
scaleSpace-method	Class '"Scale4C"'
scaleSpace<-	Class '"Scale4C"'
scaleSpace<--method	Class '"Scale4C"'
singularities	Class '"Scale4C"'
singularities-method	Class '"Scale4C"'
singularities<-	Class '"Scale4C"'
singularities<--method	Class '"Scale4C"'
viewpoint	Class '"Scale4C"'
viewpoint-method	Class '"Scale4C"'
viewpoint<-	Class '"Scale4C"'
viewpoint<--method	Class '"Scale4C"'
viewpointChromosome	Class '"Scale4C"'
viewpointChromosome-method	Class '"Scale4C"'
viewpointChromosome<-	Class '"Scale4C"'
viewpointChromosome<--method	Class '"Scale4C"'