onehot_vectorizer {kmers} R Documentation

make the sequence embedding via the one-hot encoding(Bag-of-n-grams) of

Description

the k-mer composition

Usage

onehot_vectorizer(x,
    type = Protein,
    k = 6);

Arguments

x

should be a collection of the FastaSeq sequence collection, which can be a FastaFile object, a vector of the FastaSeq object, or a character vector of the raw sequence data.

type

the sequence data type, default is protein sequence. If the sequence type is not protein, then the input sequence data will be canonicalized as the standard nucleotide letters at first. [as SeqTypes]

k

the length of the k-mers. [as integer]

env

the R# runtime environment object. [as Environment]

Details

unlike the tfidf_vectorizer api, which evaluates the weight of each k-mer term by the term frequency and the inverse document frequency, this api just encodes the k-mer composition of the sequence data as a binary vector, i.e. the presence or absence of each k-mer term.

Authors

seqtoolkit

Value

a data frame object: each row is a sequence in the input sequence collection(the row name is the fasta title of the corresponding sequence), and each column is a k-mer term, the cell value is ONE when the k-mer is exists in the corresponding sequence, otherwise ZERO.

this function returns NULL if the input data can not be cast to a fasta sequence collection.

clr value class

Examples

[Package kmers version 1.0.0.0 Index]