encodeKMerSeq

A number indicating k-mer sequence encoding

A DNAStringSet object of the inputted fasta file

dnaStringSet


DNAshapeR can be used to generate feature vectors for a user-defined model.
The model can be a k-mer sequence. Sequence is encoded in four binary
features (i.e., in terms of 1-mers, 0001 for adenine, 0010 for cytosine,
0100 for guanine, and 1000 for thymine) at each nucleotide position
(Zhou, et al., 2015). The function permits an encoding of 2-mers and 3-mers
(16 and 64 binary features at each position, respectively).


DNAhapeR is an R/BioConductor package for ultra-fast,
high-throughput predictions of DNA shape features.
The package allows to predict,
visualize and encode DNA shape features
for statistical learning.

TsuPei Chiu

DNAshapeR

High-throughput prediction of DNA shape features

encodeKMerSeq function

DNAshapeR can be used to generate feature vectors for a user-defined model.
The model can be a k-mer sequence. Sequence is encoded in four binary
features (i.e., in terms of 1-mers, 0001 for adenine, 0010 for cytosine,
0100 for guanine, and 1000 for thymine) at each nucleotide position
(Zhou, et al., 2015). The function permits an encoding of 2-mers and 3-mers
(16 and 64 binary features at each position, respectively).

encodeKMerSeq: Encode k-mer DNA sequence features

Description

Usage

Arguments

Value