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