run the CD-HIT like sequence clustering and then export the cluster

cdhit_clusters {kmers}

R Documentation

run the CD-HIT like sequence clustering and then export the cluster

Description

result as a set of the cluster tables

Usage

cdhit_clusters(x,
    k = 12,
    identities = 0.8,
    n.threads = NULL);

Arguments

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

the k-mer size for build the min-hash sketch of the sequence data:

protein - k=5aa
nucleotide - k=12nt
genomics - k=31nt

identities

the sequence identity threshold of the cluster members: the sequences that their identity is greater than or equals to this threshold value will be clustered into the same cluster. [as double]

n.threads

the thread number for run the min-hash task in parallel. [as integer]

env

the R# runtime environment object. [as Environment]

Authors

seqtoolkit

Value

a tuple list that contains the data slots:

family: a vector of the FamilyExports object, each element is the summary data of one cluster: the family_id, the members cluster size, and the representative/rep_seq data of the representative sequence;
sequence: a vector of the SequenceCluster object, each element is the data of one cluster member: the seq_title, the family_id, the score identity to the cluster representative and the seq sequence data;
clusters: a vector of the SimilarHit object, which is the raw cluster result of the CD-HIT like clustering: the SeqID is the representative sequence of the cluster and the Similar property is the identity score of each cluster member to the representative sequence.

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

clr value class

any kind

[Package kmers version 1.0.0.0 Index]