generate sequence k-mer count data matrix

kmers_matrix {kmers}

R Documentation

generate sequence k-mer count data matrix

Description

Usage

kmers_matrix(x,
    k = 3);

Arguments

a collection of the sequence data, which can be a fasta sequence collection(FastaSeq, FastaFile), a fastq sequence collection(FastQFile) or any other @T:SMRUCC.genomics.SequenceModel.FASTA.IFastaProvider

k

[as integer]

env

[as Environment]




        Details

        

        Authors

        seqtoolkit

        Value

        a Matrix k-mer count matrix object: each row in this matrix is a sequence in the input sequence collection(the row name is the sequence title), and each column is a k-mer feature(the sampleID property of the generated matrix is the k-mer alphabet sorted in ascending order), the cell value is the count of the corresponding k-mer in the corresponding sequence(ZERO means that the k-mer is not exists in the target sequence).

this function returns a R# error message object if the input data can not be cast to a collection of the sequence data.
clr value class
Matrix

        Examples

        

        
        [Package kmers version 1.0.0.0 Index]