Automated Phylogenetic Sequence Cluster Identification from 'GenBank'


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Documentation for package ‘phylotaR’ version 1.0.0

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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