clstr_subtree: Cluster all sequences descending from a txid

In ropensci/phylotaR: Automated Phylogenetic Sequence Cluster Identification from 'GenBank'

Cluster all sequences descending from a txid

Description

Identifies clusters from sequences associated with a txid and all its descendants. Clusters returned by this function will thus be of cl_type 'subtree'.

Usage

clstr_subtree(txid, sqs, txdct, dds, ps, lvl)

Arguments

txid	Taxonomic ID
sqs	Sequence object of all downloaded sequences
txdct	Taxonomic dictionary
dds	Vector of direct descendants
ps	Parameters list, generated with parameters()
lvl	Integer, number of message indentations indicating code depth.

Value

ClstrArc

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(), clstr2_calc(), clstr_all(), clstr_direct(), clstr_sqs(), 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 July 9, 2023, 3:17 p.m.