Return taxonomic IDs for a vector of sequence IDs or all sequences in a cluster. User can specify what rank the IDs should be returned. If NULL, the lowest level is returned.
Details
txids can either be provided by user or they can be determined for a vector of sids or for a cid. If keep_higher is TRUE, any sequence that has a identity that is higher than the given rank will be returned. If FALSE, these sequences will return ”.
See also
Other tools-public:
calc_mad(),
calc_wrdfrq(),
drop_by_rank(),
drop_clstrs(),
drop_sqs(),
get_clstr_slot(),
get_nsqs(),
get_ntaxa(),
get_sq_slot(),
get_stage_times(),
get_tx_slot(),
is_txid_in_clstr(),
is_txid_in_sq(),
list_clstrrec_slots(),
list_ncbi_ranks(),
list_seqrec_slots(),
list_taxrec_slots(),
plot_phylota_pa(),
plot_phylota_treemap(),
read_phylota(),
write_sqs()
Examples
data('bromeliads')
# get all the genus IDs and names
genus_ids <- get_txids(phylota = bromeliads, txids = bromeliads@txids,
rnk = 'genus')
genus_ids <- unique(genus_ids)
# drop empty IDs -- this happens if a given lineage has no ID for specified rank
genus_ids <- genus_ids[genus_ids != '']
# get names
(get_tx_slot(phylota = bromeliads, txid = genus_ids, slt_nm = 'scnm'))
#> 100680 2815862 2815856 2707094
#> "Cottendorfia" "Karawata" "Pseudaraeococcus" "Wittmackia"
#> 2184980 2184933 2184932 2184931
#> "Forzzaea" "Sincoraea" "Rokautskyia" "Hoplocryptanthus"
#> 1387303 1349361 796805 713961
#> "Lapanthus" "Canistropsis" "Disteganthus" "Eduandrea"
#> 326799 326795 326788 213064
#> "Portea" "Hohenbergiopsis" "Fernseea" "Edmundoa"
#> 106462 106458 106452 106447
#> "Ochagavia" "Neoglaziovia" "Greigia" "Fascicularia"
#> 106440 106438 106430 106424
#> "Deinacanthon" "Chevaliera" "Androlepis" "Acanthostachys"
#> 49536 49531 49529 49522
#> "Wittrockia" "Ronnbergia" "Quesnelia" "Orthophytum"
#> 49520 49512 49496 49493
#> "Nidularium" "Lymania" "Cryptanthus" "Canistrum"
#> 49491 49476 15119 15114
#> "Hohenbergia" "Araeococcus" "Billbergia" "Aechmea"
#> 4616 4614 15164 100682
#> "Bromelia" "Ananas" "Puya" "Deuterocohnia"
#> 49487 49526 49483 49485
#> "Fosterella" "Pitcairnia" "Dyckia" "Encholirium"
#> 49516 222987 15141 2821261
#> "Navia" "Brewcaria" "Hechtia" "Bakerantha"
#> 2821262 261216 49479 106432
#> "Mesoamerantha" "Lindmania" "Brocchinia" "Ayensua"
#> 49534 49518 213045 1908703
#> "Vriesea" "Neoregelia" "Werauhia" "Lutheria"
#> 49514 106428 1908700 1908698
#> "Mezobromelia" "Alcantarea" "Jagrantia" "Goudaea"
#> 1908705 2969759 1908706 1908701
#> "Stigmatodon" "Hylaeaicum" "Zizkaea" "Josemania"
#> 2002971 15170 294096 49489
#> "Waltillia" "Tillandsia" "Viridantha" "Guzmania"
#> 106471 1908553 1908702 1908697
#> "Racinaea" "Wallisia" "Lemeltonia" "Barfussia"
#> 1908704 1908699 15123 15137
#> "Pseudalcantarea" "Gregbrownia" "Catopsis" "Glomeropitcairnia"