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.
Arguments
- phylota
Phylota object
- cid
Cluster ID
- sid
Sequence ID(s)
- txids
Vector of txids
- rnk
Taxonomic rank
- keep_higher
Keep higher taxonomic IDs?
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"