clstr2_calc: Cluster sets of clusters identified in cluster stage

Description Usage Arguments See Also

View source: R/stage4.R

Description

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.

Usage

1

Arguments

ps

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.