clstr2_calc: Cluster sets of clusters identified in cluster stage

Description Usage Arguments See Also

View source: R/stage4.R


Loads cluster sets from cache. Extracts seed sequences and runs all-v-all BLAST of seeds to identify sister clusters. Sisters are then merged. An object of all sequences and clusters is then saved in cache.





Parameters list, generated with parameters()

See Also

Other run-private: batcher, blast_clstr, blast_filter, blast_setup, blast_sqs, blastcache_load, blastcache_save, blastdb_gen, blastn_run, cache_rm, cache_setup, clade_select, clstr_all, clstr_direct, clstr_sqs, clstr_subtree, clstrarc_gen, clstrarc_join, clstrrec_gen, clstrs_calc, clstrs_join, clstrs_merge, clstrs_renumber, clstrs_save, cmdln, descendants_get, download_obj_check, error, gb_extract, hierarchic_download, info, ncbicache_load, ncbicache_save, obj_check, obj_load, obj_save, outfmt_get, parameters_load, parameters_setup, parent_get, progress_init, progress_read, progress_reset, progress_save, rank_get, rawseqrec_breakdown, safely_connect, search_and_cache, searchterm_gen, seeds_blast, seq_download, seqarc_gen, seqrec_augment, seqrec_convert, seqrec_gen, seqrec_get, sids_check, sids_get, sids_load, sids_save, sqs_count, sqs_save, stage_args_check, stages_run, tax_download, taxdict_gen, taxtree_gen, txids_get, txnds_count, warn

ropensci/phylotaR documentation built on Jan. 16, 2020, 11:47 a.m.