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

## Documentation for package ‘Scale4C’ version 1.0.0

- 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"'