phylotaR (version 1.0.0)

clusters2_run: Run the cluster2 stage

Description

Run the fourth stage of the phylotaR pipeline, cluster2. Identify clusters at higher taxonomic levels by merging sister clusters.

Usage

clusters2_run(wd)

Arguments

wd

Working directory

See Also

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

Examples

# 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)
# }