vsearch_clustering | R Documentation |
physeq
or cluster a list of DNA sequences using vsearch softwarevsearch_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
)
physeq |
(required): a |
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
|
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 |
vsearch_cluster_method |
(default: "–cluster_size) See other possible
methods in the vsearch manual (e.g.
|
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 ?
|
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.
A new object of class physeq
or a list of cluster if dna_seq
args was used.
Adrien Taudière
VSEARCH can be downloaded from https://github.com/torognes/vsearch. More information in the associated publication https://pubmed.ncbi.nlm.nih.gov/27781170.
asv2otu()
, swarm_clustering()
summary_plot_pq(data_fungi)
d_vs <- vsearch_clustering(data_fungi)
summary_plot_pq(d_vs)
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