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

[Up] [Top]

Documentation for package ‘Scale4C’ version 1.9.0

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"'