# Automated Phylogenetic Sequence Cluster Identification from 'GenBank'

## Documentation for package ‘phylotaR’ version 1.0.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

A B C D E G H I L M N O P R S T U W Y misc

## -- A --

aotus | Example phylota object (aotus)
as.character-method | Cluster record archive
as.character-method | Cluster record
as.character-method | Phylota object
as.character-method | Sequence record archive
as.character-method | Sequence record
as.character-method | Taxonomic record dictionary
as.character-method | Taxonomic record

## -- B --

batcher | Download in batches
blastcache_load | Load BLAST results from cache
blastcache_save | Save BLAST results to cache
blastdb_gen | Generate a BLAST database
blastn_run | Launch blastn
blast_clstr | Cluster BLAST Results
blast_filter | Filter BLAST results
blast_setup | Ensures NCBI BLAST tools are installed
blast_sqs | BLAST All vs All
bromeliads | Example phylota object (bromeliads)

## -- C --

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
ClstrArc-class | Cluster record archive
ClstrArc-method | Cluster record archive
clstrarc_gen | Generate cluster archive container class
clstrarc_join | Join two cluster archive
ClstrRec-class | Cluster record
ClstrRec-method | 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
clstrs_renumber | Renumber cluster IDs
clstrs_save | Save clusters to cache
clstr_all | Hierarchically cluster all sequences of a txid
clstr_direct | Cluster sequences directly associated with txid
clstr_sqs | Identify clusters from sequences
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)

## -- D --

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

## -- E --

error | Write error message to log

## -- G --

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

## -- H --

hierarchic_download | Hierarchically get sequences for a txid

## -- I --

info | Write info message to log
is_txid_in_clstr | Is txid in cluster?
is_txid_in_sq | Is txid in sequence?

## -- L --

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

## -- M --

mk_txid_in_sq_mtrx | Return matrix of txid in sequence

## -- N --

ncbicache_load | Retrieve cached NCBI query
ncbicache_save | Save NCBI query result to cache

## -- O --

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

## -- P --

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
Phylota-method | Phylota object
plot_phylota_pa | Plot presence/absence matrix
plot_phylota_treemap | Plot treemap of Phylota object
print-method | Cluster record archive
print-method | Cluster record
print-method | Phylota object
print-method | Sequence record archive
print-method | Sequence record
print-method | Taxonomic record dictionary
print-method | Taxonomic record
progress_init | Initialise progress list in cache
progress_read | Read the progress from cache
progress_reset | Reset progress
progress_save | Save current progress

## -- R --

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

## -- S --

safely_connect | Safely run rentrez function
searchterm_gen | Construct GenBank Search Term
search_and_cache | Run rentrez function and cache results
seeds_blast | BLAST seed sequences
SeqArc-class | Sequence record archive
SeqArc-method | Sequence record archive
seqarc_gen | Generate sequence archive
SeqRec-class | Sequence record
SeqRec-method | Sequence record
seqrec_augment | Augment sequence records list
seqrec_convert | Convert raw Entrez gbwithparts record to SeqRecs
seqrec_gen | Generate sequence record
seqrec_get | seqrec_get
seq_download | Download sequences for txids
setup | Set-up parameters
show-method | Cluster record archive
show-method | Cluster record
show-method | Phylota object
show-method | Sequence record archive
show-method | Sequence record
show-method | Taxonomic record dictionary
show-method | Taxonomic record
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
stages_run | Sequentially run each stage
stage_args_check | Check stage arguments
str-method | Cluster record archive
str-method | Cluster record
str-method | Phylota object
str-method | Sequence record archive
str-method | Sequence record
str-method | Taxonomic record dictionary
str-method | Taxonomic record
sturgeons | Example phylota object (sturgeons)
summary-method | Cluster record archive
summary-method | Cluster record
summary-method | Phylota object
summary-method | Sequence record archive
summary-method | Sequence record
summary-method | Taxonomic record dictionary
summary-method | Taxonomic record
summary_phylota | Summarise clusters in Phylota Table

## -- T --

tardigrades | Example phylota object (tardigrades)
TaxDict-class | Taxonomic record dictionary
TaxDict-method | Taxonomic record dictionary
taxdict_gen | Generate taxonomic dictionary
taxise_run | Run taxise stage
TaxRec-class | Taxonomic record
TaxRec-method | Taxonomic record
taxtree_gen | Generate taxonomic tree
tax_download | Download taxonomic records
tinamous | Example phylota object (tinamous)
txids_get | Searches for descendant taxonomic IDs
txnds_count | Count number of descending taxonomic nodes

## -- U --

update_phylota | Update slots

## -- W --

warn | Write warning message to log
write_sqs | Write out sequences

## -- Y --

yeasts | Example phylota object (yeasts)

## -- misc --

[-method | Cluster record archive
[-method | Sequence record archive
[[-method | Cluster record archive
[[-method | Phylota object
[[-method | Sequence record archive