swarm_clustering | R Documentation |
physeq
or cluster a list of DNA sequences using SWARMswarm_clustering(
physeq = NULL,
dna_seq = NULL,
d = 1,
swarmpath = "swarm",
vsearch_path = "vsearch",
nproc = 1,
swarm_args = "--fastidious",
tax_adjust = 0,
keep_temporary_files = FALSE
)
physeq |
(required): a |
dna_seq |
NOT WORKING FOR THE MOMENT
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
|
d |
(default: 1) maximum number of differences allowed between two
amplicons, meaning that two amplicons will be grouped if they have |
swarmpath |
(default: swarm) path to swarm |
vsearch_path |
(default: vsearch) path to vsearch, used only if physeq is NULL and dna_seq is provided. |
nproc |
(default: 1) Set to number of cpus/processors to use for the clustering |
swarm_args |
(default : "–fastidious") a one length character element defining other parameters to passed on to swarm See other possible methods in the SWARM pdf manual |
tax_adjust |
(Default 0) See the man page
of |
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 SWARM.
A new object of class physeq
or a list of cluster if dna_seq
args was used.
SWARM can be downloaded from https://github.com/torognes/swarm/.
SWARM can be downloaded from https://github.com/torognes/swarm. More information in the associated publications \Sexpr[results=rd]{tools:::Rd_expr_doi("doi:10.1093/bioinformatics/btab493")} and \Sexpr[results=rd]{tools:::Rd_expr_doi("doi:10.7717/peerj.593")}
asv2otu()
, vsearch_clustering()
summary_plot_pq(data_fungi)
system2("swarm", "-h")
data_fungi_swarm <- swarm_clustering(data_fungi)
summary_plot_pq(data_fungi_swarm)
sequences_ex <- c(
"TACCTATGTTGCCTTGGCGGCTAAACCTACCCGGGATTTGATGGGGCGAATTAATAACGAATTCATTGAATCA",
"TACCTATGTTGCCTTGGCGGCTAAACCTACCCGGGATTTGATGGGGCGAATTACCTGGTAAGGCCCACTT",
"TACCTATGTTGCCTTGGCGGCTAAACCTACCCGGGATTTGATGGGGCGAATTACCTGGTAGAGGTG",
"TACCTATGTTGCCTTGGCGGCTAAACCTACC",
"CGGGATTTGATGGCGAATTACCTGGTATTTTAGCCCACTTACCCGGTACCATGAGGTG",
"GCGGCTAAACCTACCCGGGATTTGATGGCGAATTACCTGG",
"GCGGCTAAACCTACCCGGGATTTGATGGCGAATTACAAAG",
"GCGGCTAAACCTACCCGGGATTTGATGGCGAATTACAAAG",
"GCGGCTAAACCTACCCGGGATTTGATGGCGAATTACAAAG"
)
sequences_ex_swarm <- swarm_clustering(
dna_seq = sequences_ex
)
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