Create algorithm for make sequence embedding

seq_sgt {bioseq.fasta}

R Documentation

Create algorithm for make sequence embedding

Description

Usage

seq_sgt(
    moltype = Protein,
    kappa = 1,
    lengthsensitive = FALSE);

Arguments

moltype

the molecule type of the target sequence data for make the sequence embedding: protein, DNA or RNA sequence. [as SeqTypes]

kappa

the decay factor of the sequence graph transform algorithm, the smaller value of this parameter makes the far distance k-mer composition weight less. [as double]

lengthsensitive

is the generated embedding vector sensitive to the sequence length? if this parameter is FALSE(the default value), then the embedding vector will be normalized by the sequence length, so that two sequences with the same k-mer composition but different lengths get the same embedding vector; if this parameter is TRUE, then the vector norm value grows with the sequence length. [as boolean]

Authors

seqtoolkit

Value

a CreateMatrix algorithm object for embedding the given sequence data as a numeric vector, which can be applied on a collection of the sequence data via the seq_vector api.

clr value class

CreateMatrix

[Package bioseq.fasta version 1.0.0.0 Index]