PredictionProfileAccessors {kebabs} | R Documentation |
PredictionProfile Accessors
## S4 method for signature 'PredictionProfile' sequences(object)
object |
a prediction profile object |
sequences
: sequences for which profiles were generated
profiles
: prediction profiles
baselines
: baselines for the plot, this is the model offset
distributed to all sequence positions
sequences
:
return the sequences.
profiles
:
return the prediction profiles.
baselines
:
return the baselines.
x[i]
:
return a PredictionProfile
object that only contains the
prediction profiles selected with the subsetting parameter i
. This
parameter can be a numeric vector with indices or a character vector with
sample names.
Johannes Palme <kebabs@bioinf.jku.at>
http://www.bioinf.jku.at/software/kebabs
J. Palme, S. Hochreiter, and U. Bodenhofer (2015) KeBABS: an R package
for kernel-based analysis of biological sequences.
Bioinformatics, 31(15):2574-2576, 2015.
DOI: 10.1093/bioinformatics/btv176.
## create kernel object for gappy pair kernel gappy <- gappyPairKernel(k=1,m=11, annSpec=TRUE) ## Not run: ## load data data(CCoil) ## perform training - feature weights are computed by default model <- kbsvm(ccseq, yCC, gappya, pkg="LiblineaR", svm="C-svc", cost=15) ## compute prediction profiles predProf <- getPredictionProfile(ccseq, gappya, featureWeights(model), modelOffset(model)) predProf15 <- predProf[c(1,5),] sequences(predProf15) profiles(predProf15) baselines(predProf15) ## End(Not run)