Man pages for phylotaR
Automated Phylogenetic Sequence Cluster Identification from 'GenBank'

aotusExample phylota object (aotus)
batcherDownload in batches
blastcache_loadLoad BLAST results from cache
blastcache_saveSave BLAST results to cache
blast_clstrCluster BLAST Results
blastdb_genGenerate a BLAST database
blast_filterFilter BLAST results
blastn_runLaunch blastn
blast_setupEnsures NCBI BLAST tools are installed
blast_sqsBLAST All vs All
bromeliadsExample phylota object (bromeliads)
cache_rmDelete a cache
cache_setupSet-up a cache
calc_madCalculate MAD score
calc_wrdfrqCalculate word frequencies
clade_selectGet all node IDs that will be processed
clstr2_calcCluster sets of clusters identified in cluster stage
clstr_allHierarchically cluster all sequences of a txid
ClstrArc-classCluster record archive
clstrarc_genGenerate cluster archive container class
clstrarc_joinJoin two cluster archive
clstr_directCluster sequences directly associated with txid
ClstrRec-classCluster record
clstrrec_genGenerate list of clusters
clstrs_calcCalculate clusters for all sequences in wd
clstrs_joinJoin clusters for merging
clstrs_mergeMerge joined clusters
clstr_sqsIdentify clusters from sequences
clstrs_renumberRenumber cluster IDs
clstrs_saveSave clusters to cache
clstr_subtreeCluster all sequences descending from a txid
clusters2_runRun the cluster2 stage
clusters_runRun the cluster stage
cmdlnRun a command via terminal/command prompt
cycadsExample phylota object (cycads)
descendants_getGet descendants
download_obj_checkCheck an object returned from rentrez function
download_runRun download stage
dragonfliesExample phylota object (dragonflies)
drop_by_rankReduce clusters to specific rank
drop_clstrsDrop cluster records from phylota object
drop_sqsDrop sequences in a cluster
errorWrite error message to log
get_clstr_slotGet slot data for each cluster record
get_nsqsCount number of sequences
get_ntaxaCount number of unique taxa
get_sq_slotGet slot data for each sequence
get_stage_timesGet run times for different stages
get_txidsGet taxonomic IDs by rank
get_tx_slotGet slot data for each taxon record
hierarchic_downloadHierarchically get sequences for a txid
infoWrite info message to log
is_txid_in_clstrIs txid in cluster?
is_txid_in_sqIs txid in sequence?
list_clstrrec_slotsList all ClstrRec slots
list_ncbi_ranksList all NCBI Ranks
list_seqrec_slotsList all SeqRec slots
list_taxrec_slotsList all TaxRec slots
mk_txid_in_sq_mtrxReturn matrix of txid in sequence
ncbicache_loadRetrieve cached NCBI query
ncbicache_saveSave NCBI query result to cache
obj_checkCheck if an object exists
obj_loadLoad a named object from the cache
obj_saveSave a named object in the cache
parametersDefault parameters
parameters_loadLoad parameters from cache
parameters_resetChange parameters in a working directory
parameters_setupSet Up Parameters
parent_getGet taxonomic parent
Phylota-classPhylota object
plot_phylota_paPlot presence/absence matrix
plot_phylota_treemapPlot treemap of Phylota object
progress_initInitialise progress list in cache
progress_readRead the progress from cache
progress_resetReset progress
progress_saveSave current progress
rank_getGet rank
read_phylotaGenerate a Phylota object in R
resetReset a phylotaR pipeline run
restartRestart a phylotaR pipeline run
runRun phylotaR pipeline
safely_connectSafely run rentrez function
search_and_cacheRun rentrez function and cache results
searchterm_genConstruct GenBank Search Term
seeds_blastBLAST seed sequences
SeqArc-classSequence record archive
seqarc_genGenerate sequence archive
seq_downloadDownload sequences for txids
seqrec_augmentAugment sequence records list
SeqRec-classSequence record
seqrec_convertConvert raw Entrez gbwithparts record to SeqRecs
seqrec_genGenerate sequence record
setupSet-up parameters
sids_checkCheck if sids exist
sids_getReturn random set of sequence IDs
sids_loadLoad sids from cache
sids_saveSave sids to cache
sqs_countCount number of sequences for txid
sqs_loadLoad sequences from cache
sqs_saveSave sequences to cache
stage_args_checkCheck stage arguments
stages_runSequentially run each stage
sturgeonsExample phylota object (sturgeons)
summary_phylotaSummarise clusters in Phylota Table
tardigradesExample phylota object (tardigrades)
TaxDict-classTaxonomic record dictionary
taxdict_genGenerate taxonomic dictionary
tax_downloadDownload taxonomic records
taxise_runRun taxise stage
TaxRec-classTaxonomic record
taxtree_genGenerate taxonomic tree
tinamousExample phylota object (tinamous)
txids_getSearches for descendant taxonomic IDs
txnds_countCount number of descending taxonomic nodes
update_phylotaUpdate slots
warnWrite warning message to log
write_sqsWrite out sequences
yeastsExample phylota object (yeasts)
phylotaR documentation built on July 31, 2018, 5:01 p.m.