cdhit_nr {kmers} R Documentation

run the CD-HIT like sequence clustering for get the non-redundant

Description

sequence set

Usage

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

Arguments

x

a collection of the sequence data for run the clustering, which can be a FastaFile object, a vector of the @T:SMRUCC.genomics.SequenceModel.FASTA.FastaSeq

k

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

identities

[as double]

n.threads

[as integer]

env

[as Environment]

Details

the input sequence data will be sorted by the sequence length in descending order at first, and then the greedy clustering algorithm runs based on the min-hash similarity of the k-mer sketch of each sequence.

Authors

seqtoolkit

Value

a vector of the FastaSeq sequence object: the representative sequence of each cluster. For a cluster that contains multiple sequence members, the fasta headers of the representative sequence is formatted as: the representative sequence title, {cluster_size} cluster members and the json text of the cluster member sequence id list; and the sequence data of a singleton cluster(the unique sequence) is returned as is.

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]