Skip to contents

Running

Functions for starting/stopping the phylotaR pipeline.

setup()
Set-up parameters
run()
Run phylotaR pipeline
restart()
Restart a phylotaR pipeline run
reset()
Reset a phylotaR pipeline run
parameters()
Default parameters
parameters_reset()
Change parameters in a working directory
taxise_run()
Run taxise stage
download_run()
Run download stage
clusters_run()
Run the cluster stage
clusters2_run()
Run the cluster2 stage

Tools

Tools for interacting with the Phylota object

read_phylota()
Generate a Phylota object in R
drop_by_rank()
Reduce clusters to specific rank
drop_clstrs()
Drop cluster records from phylota object
drop_sqs()
Drop sequences in a cluster
get_clstr_slot()
Get slot data for each cluster record
get_sq_slot()
Get slot data for each sequence
get_tx_slot()
Get slot data for each taxon record
get_nsqs()
Count number of sequences
get_ntaxa()
Count number of unique taxa
get_txids()
Get taxonomic IDs by rank
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
calc_wrdfrq()
Calculate word frequencies
calc_mad()
Calculate MAD score
write_sqs()
Write out sequences
plot_phylota_treemap()
Plot treemap of Phylota object
plot_phylota_pa()
Plot presence/absence matrix
get_stage_times()
Get run times for different stages

Data

Example Phylota objects

aotus
Example phylota object (aotus)
bromeliads
Example phylota object (bromeliads)
cycads
Example phylota object (cycads)
dragonflies
Example phylota object (dragonflies)
sturgeons
Example phylota object (sturgeons)
tardigrades
Example phylota object (tardigrades)
tinamous
Example phylota object (tinamous)
yeasts
Example phylota object (yeasts)

Classes

S4 classes

Taxise (private)

Internal functions for running the taxise stage, use phylotaR::: to access.

rank_get()
Get rank
descendants_get()
Get descendants
sqs_count()
Count number of sequences for txid
clade_select()
Get all node IDs that will be processed
txnds_count()
Count number of descending taxonomic nodes
txids_get()
Searches for descendant taxonomic IDs
parent_get()
Get taxonomic parent
tax_download()
Download taxonomic records
taxdict_gen()
Generate taxonomic dictionary
taxtree_gen()
Generate taxonomic tree

Download (private)

Internal functions for running the download stage, use phylotaR::: to access.

searchterm_gen()
Construct GenBank Search Term
seq_download()
Download sequences for txids
seqarc_gen()
Generate sequence archive
seqrec_augment()
Augment sequence records list
seqrec_convert()
Convert raw Entrez gb text record to SeqRecs
seqrec_gen()
Generate sequence record
seqrec_get()
seqrec_get
hierarchic_download()
Hierarchically get sequences for a txid
sids_get()
Return random set of sequence IDs
outfmt_get()
Determine 'outformat' format

Cluster (private)

Internal functions for running the cluster stage, use phylotaR::: to access.

blast_clstr()
Cluster BLAST Results
blast_filter()
Filter BLAST results
blast_sqs()
BLAST All vs All
blastdb_gen()
Generate a BLAST database
blastn_run()
Launch blastn
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
clstrarc_gen()
Generate cluster archive container class
clstrarc_join()
Join two cluster archive
clstrrec_gen()
Generate list of clusters
clstrs_calc()
Calculate clusters for all sequences in wd

Cluster2 (private)

Internal functions for running the cluster2 stage, use phylotaR::: to access.

seeds_blast()
BLAST seed sequences
clstr2_calc()
Cluster sets of clusters identified in cluster stage
clstrs_join()
Join clusters for merging
clstrs_merge()
Merge joined clusters
clstrs_renumber()
Renumber cluster IDs

Misc (private)

Miscellaneous internal functions, use phylotaR::: to access.

blast_setup()
Ensures NCBI BLAST tools are installed
download_obj_check()
Check an object returned from rentrez function
safely_connect()
Safely run rentrez function
search_and_cache()
Run rentrez function and cache results
batcher()
Download in batches
info()
Write info message to log
error()
Write error message to log
warn()
Write warning message to log
blastcache_load()
Load BLAST results from cache
blastcache_save()
Save BLAST results to cache
sids_check()
Check if sids exist
sids_load()
Load sids from cache
sids_save()
Save sids to cache
cache_rm()
Delete a cache
cache_setup()
Set-up a cache
sqs_save()
Save sequences to cache
ncbicache_load()
Retrieve cached NCBI query
ncbicache_save()
Save NCBI query result to cache
stages_run()
Sequentially run each stage
stage_args_check()
Check stage arguments
mk_txid_in_sq_mtrx()
Return matrix of txid in sequence
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
summary_phylota()
Summarise clusters in Phylota Table
parameters_load()
Load parameters from cache
progress_init()
Initialise progress list in cache
progress_read()
Read the progress from cache
progress_reset()
Reset progress
progress_save()
Save current progress
cmdln()
Run a command via terminal/command prompt
update_phylota()
Update slots
parameters_setup()
Set Up Parameters
clstrs_save()
Save clusters to cache
gb_extract()
Extract elements from a raw GenBank record
rawseqrec_breakdown()
Breakdown a sequence record into its features