Man pages for phylotaR
Automated Phylogenetic Sequence Cluster Identification from 'GenBank'
| aotus | Example phylota object (aotus) |
| batcher | Download in batches |
| blastcache_load | Load BLAST results from cache |
| blastcache_save | Save BLAST results to cache |
| blast_clstr | Cluster BLAST Results |
| blastdb_gen | Generate a BLAST database |
| blast_filter | Filter BLAST results |
| blastn_run | Launch blastn |
| blast_setup | Ensures NCBI BLAST tools are installed |
| blast_sqs | BLAST All vs All |
| bromeliads | Example phylota object (bromeliads) |
| cache_rm | Delete a cache |
| cache_setup | Set-up a cache |
| calc_mad | Calculate MAD score |
| calc_wrdfrq | Calculate word frequencies |
| clade_select | Get all node IDs that will be processed |
| clstr2_calc | Cluster sets of clusters identified in cluster stage |
| clstr_all | Hierarchically cluster all sequences of a txid |
| ClstrArc-class | Cluster record archive |
| clstrarc_gen | Generate cluster archive container class |
| clstrarc_join | Join two cluster archive |
| clstr_direct | Cluster sequences directly associated with txid |
| ClstrRec-class | Cluster record |
| clstrrec_gen | Generate list of clusters |
| clstrs_calc | Calculate clusters for all sequences in wd |
| clstrs_join | Join clusters for merging |
| clstrs_merge | Merge joined clusters |
| clstr_sqs | Identify clusters from sequences |
| clstrs_renumber | Renumber cluster IDs |
| clstrs_save | Save clusters to cache |
| clstr_subtree | Cluster all sequences descending from a txid |
| clusters2_run | Run the cluster2 stage |
| clusters_run | Run the cluster stage |
| cmdln | Run a command via terminal/command prompt |
| cycads | Example phylota object (cycads) |
| descendants_get | Get descendants |
| download_obj_check | Check an object returned from rentrez function |
| download_run | Run download stage |
| dragonflies | Example phylota object (dragonflies) |
| drop_by_rank | Reduce clusters to specific rank |
| drop_clstrs | Drop cluster records from phylota object |
| drop_sqs | Drop sequences in a cluster |
| error | Write error message to log |
| get_clstr_slot | Get slot data for each cluster record |
| get_nsqs | Count number of sequences |
| get_ntaxa | Count number of unique taxa |
| get_sq_slot | Get slot data for each sequence |
| get_stage_times | Get run times for different stages |
| get_txids | Get taxonomic IDs by rank |
| get_tx_slot | Get slot data for each taxon record |
| hierarchic_download | Hierarchically get sequences for a txid |
| info | Write info message to log |
| is_txid_in_clstr | Is txid in cluster? |
| is_txid_in_sq | Is txid in sequence? |
| list_clstrrec_slots | List all ClstrRec slots |
| list_ncbi_ranks | List all NCBI Ranks |
| list_seqrec_slots | List all SeqRec slots |
| list_taxrec_slots | List all TaxRec slots |
| mk_txid_in_sq_mtrx | Return matrix of txid in sequence |
| ncbicache_load | Retrieve cached NCBI query |
| ncbicache_save | Save NCBI query result to cache |
| obj_check | Check if an object exists |
| obj_load | Load a named object from the cache |
| obj_save | Save a named object in the cache |
| parameters | Default parameters |
| parameters_load | Load parameters from cache |
| parameters_reset | Change parameters in a working directory |
| parameters_setup | Set Up Parameters |
| parent_get | Get taxonomic parent |
| Phylota-class | Phylota object |
| plot_phylota_pa | Plot presence/absence matrix |
| plot_phylota_treemap | Plot treemap of Phylota object |
| progress_init | Initialise progress list in cache |
| progress_read | Read the progress from cache |
| progress_reset | Reset progress |
| progress_save | Save current progress |
| rank_get | Get rank |
| read_phylota | Generate a Phylota object in R |
| reset | Reset a phylotaR pipeline run |
| restart | Restart a phylotaR pipeline run |
| run | Run phylotaR pipeline |
| safely_connect | Safely run rentrez function |
| search_and_cache | Run rentrez function and cache results |
| searchterm_gen | Construct GenBank Search Term |
| seeds_blast | BLAST seed sequences |
| SeqArc-class | Sequence record archive |
| seqarc_gen | Generate sequence archive |
| seq_download | Download sequences for txids |
| seqrec_augment | Augment sequence records list |
| SeqRec-class | Sequence record |
| seqrec_convert | Convert raw Entrez gbwithparts record to SeqRecs |
| seqrec_gen | Generate sequence record |
| seqrec_get | seqrec_get |
| setup | Set-up parameters |
| sids_check | Check if sids exist |
| sids_get | Return random set of sequence IDs |
| sids_load | Load sids from cache |
| sids_save | Save sids to cache |
| sqs_count | Count number of sequences for txid |
| sqs_load | Load sequences from cache |
| sqs_save | Save sequences to cache |
| stage_args_check | Check stage arguments |
| stages_run | Sequentially run each stage |
| sturgeons | Example phylota object (sturgeons) |
| summary_phylota | Summarise clusters in Phylota Table |
| tardigrades | Example phylota object (tardigrades) |
| TaxDict-class | Taxonomic record dictionary |
| taxdict_gen | Generate taxonomic dictionary |
| tax_download | Download taxonomic records |
| taxise_run | Run taxise stage |
| TaxRec-class | Taxonomic record |
| taxtree_gen | Generate taxonomic tree |
| tinamous | Example phylota object (tinamous) |
| txids_get | Searches for descendant taxonomic IDs |
| txnds_count | Count number of descending taxonomic nodes |
| update_phylota | Update slots |
| warn | Write warning message to log |
| write_sqs | Write out sequences |
| yeasts | Example phylota object (yeasts) |
