Get slot data for each sequence

Source: R/user-get.R

Get slot data for either or sequences in a cluster of a vector of sequence IDs. Use list_seqrec_slots() for a list of available slots.

get_sq_slot(phylota, cid = NULL, sid = NULL,
  slt_nm = list_seqrec_slots())

Arguments

phylota

Phylota object
cid

Cluster ID
sid

Sequence ID(s)
slt_nm

Slot name

Value

vector

See also

Other tools-public: calc_mad, calc_wrdfrq, drop_by_rank, drop_clstrs, drop_sqs, get_clstr_slot, get_nsqs, get_ntaxa, get_stage_times, get_tx_slot, get_txids, 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('aotus')
random_sid <- sample(aotus@sids, 1)
(get_sq_slot(phylota = aotus, sid = random_sid, slt_nm = 'dfln'))

#>                                                                                     AB181222.1/1555..1849 
#> "Aotus griseimembra M/LWS-14X gene for red-green sensitive visual pigment, downstream region from exon 6" 
# see list_seqrec_slots() for available slots
(list_seqrec_slots())

#>  [1] "id"      "nm"      "accssn"  "vrsn"    "url"     "txid"    "orgnsm" 
#>  [8] "dfln"    "ml_typ"  "rec_typ" "nncltds" "nambgs"  "pambgs"  "gcr"    
#> [15] "age"