PredictionProfileAccessors {kebabs} | R Documentation

## PredictionProfile Accessors

### Description

PredictionProfile Accessors

### Usage

    ## S4 method for signature 'PredictionProfile'
    sequences(object)

### Arguments

`object` | a prediction profile object

### Value

`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

### Accessor-like methods

  `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.

### Author(s)

Johannes Palme <kebabs@bioinf.jku.at>

### References

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.

### Examples

    ## 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)

[Package kebabs version 1.24.0 Index]