clusters2_run | R Documentation |
Run the fourth stage of the phylotaR pipeline, cluster2. Identify clusters at higher taxonomic levels by merging sister clusters.
clusters2_run(wd)
wd |
Working directory |
Other run-public:
ClstrArc-class
,
ClstrRec-class
,
Phylota-class
,
SeqArc-class
,
SeqRec-class
,
TaxDict-class
,
TaxRec-class
,
clusters_run()
,
parameters_reset()
,
reset()
,
restart()
,
run()
,
setup()
,
taxise_run()
## Not run:
# Note: this example requires BLAST and internet to run.
# example with temp folder
wd <- file.path(tempdir(), 'aotus')
# setup for aotus, make sure aotus/ folder already exists
if (!dir.exists(wd)) {
dir.create(wd)
}
ncbi_dr <- '[SET BLAST+ BIN PATH HERE]'
setup(wd = wd, txid = 9504, ncbi_dr = ncbi_dr) # txid for Aotus primate genus
# individually run stages
taxise_run(wd = wd)
download_run(wd = wd)
clusters_run(wd = wd)
clusters2_run(wd = wd)
## End(Not run)
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