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Recluster sequences of an object of class physeq or cluster a list of DNA sequences using vsearch software

Source: R/vsearch.R
vsearch_clustering.Rd

[Maturing]

Usage

vsearch_clustering(
  physeq = NULL,
  dna_seq = NULL,
  nproc = 1,
  id = 0.97,
  vsearchpath = "vsearch",
  tax_adjust = 0,
  vsearch_cluster_method = "--cluster_size",
  vsearch_args = "--strand both",
  keep_temporary_files = FALSE
)

Arguments

physeq

(required): a phyloseq-class object obtained using the phyloseq package.

dna_seq

You may directly use a character vector of DNA sequences in place of physeq args. When physeq is set, dna sequences take the value of physeq@refseq

nproc

(default: 1) Set to number of cpus/processors to use for the clustering

id

(default: 0.97) level of identity to cluster

vsearchpath

(default: vsearch) path to vsearch

tax_adjust

(Default 0) See the man page of merge_taxa_vec() for more details. To conserved the taxonomic rank of the most abundant ASV, set tax_adjust to 0 (default). For the moment only tax_adjust = 0 is robust

vsearch_cluster_method

(default: "--cluster_size) See other possible methods in the vsearch manual (e.g. --cluster_size or --cluster_smallmem)

  • --cluster_fast : Clusterize the fasta sequences in filename, automatically sort by decreasing sequence length beforehand.

  • --cluster_size : Clusterize the fasta sequences in filename, automatically sort by decreasing sequence abundance beforehand.

  • --cluster_smallmem : Clusterize the fasta sequences in filename without automatically modifying their order beforehand. Sequence are expected to be sorted by decreasing sequence length, unless --usersort is used. In that case you may set vsearch_args to vsearch_args = "--strand both --usersort"

vsearch_args

(default : "--strand both") a one length character element defining other parameters to passed on to vsearch.

keep_temporary_files

(logical, default: FALSE) Do we keep temporary files ?

  • temp.fasta (refseq in fasta or dna_seq sequences)

  • cluster.fasta (centroid if method = "vsearch")

  • temp.uc (clusters if method = "vsearch")

Value

A new object of class physeq or a list of cluster if dna_seq args was used.

Details

This function use the merge_taxa_vec() function to merge taxa into clusters. By default tax_adjust = 0. See the man page of merge_taxa_vec().

This function is mainly a wrapper of the work of others. Please cite vsearch.

References

VSEARCH can be downloaded from https://github.com/torognes/vsearch. More information in the associated publication https://pubmed.ncbi.nlm.nih.gov/27781170.

See also

asv2otu(), swarm_clustering()

Author

Adrien Taudière

Examples

# \donttest{
summary_plot_pq(data_fungi)
#> Cleaning suppress 0 taxa and 0 samples.

d_vs <- vsearch_clustering(data_fungi)
summary_plot_pq(d_vs)
#> Cleaning suppress 0 taxa and 0 samples.

# }