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.
Usage
get_sq_slot(phylota, cid = NULL, sid = NULL, slt_nm = list_seqrec_slots())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'))
#> AF333723.1
#> "Aotus nancymaae clone 11192.15 T-cell receptor gamma chain V-J region mRNA, partial cds"
# 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"