encodeKMerSeq: Encode k-mer DNA sequence features

In DNAshapeR: High-throughput prediction of DNA shape features

Description

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).

Usage

encodeKMerSeq(k, dnaStringSet)

Arguments

k	A number indicating k-mer sequence encoding
dnaStringSet	A DNAStringSet object of the inputted fasta file

Value

featureVector A matrix containing encoded features. Sequence feature is represented as binary numbers

Author(s)

Tsu-Pei Chiu

DNAshapeR documentation built on Nov. 8, 2020, 8:04 p.m.