build.features.kernels: Build features and kernels

In ManuSetty/ChIPKernels: String kernels for ChIP-Seq

Description

This builds the feature matrix and kernel using the dictionary. Linear kernel is computed using kernlab package.

Usage

  build.features.kernels(dictionary.file, seqs,
    kmers = NULL, kernel = FALSE, verbose = TRUE)

Arguments

dictionary.file	File containing the dictionary built using build.mismatch.dictionary or build.pw.denegerate.dictionary.
seqs	DNAStringSet representing the sequences to build the mismatch kernel. None of the sequences should contain N in the nucleotide composition
kmers	Subset of kmers to build the kernel. NULL setting uses all kmers.
kernel	Boolean indicating if the kernel should be computed. If FALSE, only the feature representation is returned.
verbose	Boolean indicating if more logs should be shown

Value

List with following elements: features Sparse feature matrix (seqs X kmers) and kernel Linear mismatch kernel.

See Also

build.mismatch.dictionary, kernelMatrix

ManuSetty/ChIPKernels documentation built on May 7, 2019, 2:46 p.m.