kebabs (version 1.2.3)

ExplicitRepresentationAccessors: ExplicitRepresentation Accessors

Description

ExplicitRepresentation Accessors

Usage

## S4 methods for signature 'ExplicitRepresentation'
## x[i,j]
## further methods see below
"%*%"(x, y)
"%*%"(x, y)

Arguments

x

an explicit representation in dense or sparse format

i

integer vector or character vector with a subset of the sample indices or names

y

in the first case and explicit representation and x is a matrix, for the second case a numeric matrix and x is an explicit representation

j

integer vector or character vector with a subset of the feature indices or names

Value

see details above

Accessor-like methods

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.

Accessor-like methods

%*%: this function provides the multiplication of a dgRMatrix or a sparse explicit representation (which is derived from dgRMatrix) with a matrix or a vector. This functionality is not available in package Matrix for a dgRMatrix.

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 (accepted). DOI: 10.1093/bioinformatics/btv176.