PredictionProfileAccessors: PredictionProfile Accessors
In kebabs: Kernel-Based Analysis Of Biological Sequences

Description Usage Arguments Value Accessor-like methods Author(s) References Examples

PredictionProfile Accessors

1 2	## 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)