taxtree_gen: Generate taxonomic tree

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

Description

Generate a taxonomic tree for easy look up of taxonomic parents and descendants.

Usage

taxtree_gen(prinds, ids, root, ps)

Arguments

prinds	Vector of integers indicating preceding node.
ids	Vector of taxonomic IDs
root	ID of root taxon
ps	Parameters list, generated with parameters()

Value

TreeMan

TreeMan class

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, 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, hierarchic_download, info, ncbicache_load, ncbicache_save, obj_check, obj_load, obj_save, parameters_load, parameters_setup, parent_get, progress_init, progress_read, progress_reset, progress_save, rank_get, 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_load, sqs_save, stage_args_check, stages_run, tax_download, taxdict_gen, txids_get, txnds_count, warn

phylotaR documentation built on May 1, 2019, 9:26 p.m.