clstr_direct: Cluster sequences directly associated with txid

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

Cluster sequences directly associated with txid

Description

In GenBank certain sequences may only be associated with a higher level taxon (e.g. genus, family ...). This function generates clusters from these sequences, alone. This function identifies such sequences in the sequence object and generates a list of clusters of cl_type 'direct'.

Usage

clstr_direct(txid, sqs, txdct, ps, lvl)

Arguments

txid	Taxonomic ID
sqs	Sequence object of all downloaded sequences
txdct	Taxonomic dictionary
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_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 July 9, 2023, 3:17 p.m.