KernelMatrixAccessors: KernelMatrix Accessors
In kebabs: Kernel-Based Analysis Of Biological Sequences

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

KernelMatrix Accessors

## S4 method for signature 'KernelMatrix,index,missing,ANY'
x[i]

## S4 method for signature 'matrix'
as.KernelMatrix(x, center = FALSE)

`x`	kernel matrix of class `KernelMatrix`
`i`	numeric vector with indicies or character with element names
`center`	when set to `TRUE` the matrix is centered. Default=FALSE

see above

: x[i,]: return a KernelMatrix object that only contains the rows selected with the subsetting parameter i. This parameter can be a numeric vector with indices or a character vector which is matched against the names of x.
: x[,j]: return a KernelMatrix object that only contains the columns selected with the subsetting parameter j. This parameter can be a numeric vector with indices or a character vector which is matched against the names of x.
: x[i,j]: return a KernelMatrix object that only contains the rows selected with the subsetting parameter i and columns selected by j. Both parameters can be a numeric vector with indices or a character vector which is matched against the names of x.

In the code snippets below, x is a kernel matrix.

: as.KernelMatrix(x, center=FALSE): center the kernel matrix dependent on the center parameter and coerce it to class KernelMatrix .

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 normalized spectrum kernel
specK5 <- spectrumKernel(k=5)
## Not run: 
## load data
data(TFBS)

km <- specK5(enhancerFB)
km1to5 <- km[1:5,1:5]
km1to5

## End(Not run)