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.

get_txids(phylota, cid = NULL, sid = NULL, txids = NULL,
  rnk = NULL, keep_higher = FALSE)

Arguments

phylota

Phylota object

cid

Cluster ID

sid

Sequence ID(s)

txids

Vector of txids

rnk

Taxonomic rank

keep_higher

Keep higher taxonomic IDs?

Value

vector

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

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 2184933 2184932 2184931 #> "Cottendorfia" "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 49487 #> "Bromelia" "Ananas" "Puya" "Fosterella" #> 49526 49485 49483 100682 #> "Pitcairnia" "Encholirium" "Dyckia" "Deuterocohnia" #> 49516 222987 15141 261216 #> "Navia" "Brewcaria" "Hechtia" "Lindmania" #> 106432 49479 106428 213045 #> "Ayensua" "Brocchinia" "Alcantarea" "Werauhia" #> 1908698 49518 49534 1908703 #> "Goudaea" "Neoregelia" "Vriesea" "Lutheria" #> 49514 1908700 2002971 1908705 #> "Mezobromelia" "Jagrantia" "Waltillia" "Stigmatodon" #> 1908701 1908706 15170 106471 #> "Josemania" "Zizkaea" "Tillandsia" "Racinaea" #> 1908553 1908702 1908697 1908704 #> "Wallisia" "Lemeltonia" "Barfussia" "Pseudalcantarea" #> 49489 1908699 15123 15137 #> "Guzmania" "Gregbrownia" "Catopsis" "Glomeropitcairnia"