is_txid_in_clstr: Is txid in cluster?

In ropensci/phylotaR: Automated Phylogenetic Sequence Cluster Identification from 'GenBank'

Is txid in cluster?

Description

Checks if given txid is represented by any of the sequences of a cluster by searching through all the sequence search organism lineages.

Usage

is_txid_in_clstr(phylota, txid, cid)

Arguments

phylota	Phylota
txid	Taxonomic ID
cid	Cluster ID

Value

boolean

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(), get_txids(), 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(tinamous)
cid <- tinamous@cids[[1]]
clstr <- tinamous[[cid]]
sq <- tinamous[[clstr@sids[[1]]]]
txid <- sq@txid
# expect true
is_txid_in_clstr(phylota = tinamous, txid = txid, cid = cid)

ropensci/phylotaR documentation built on July 9, 2023, 3:17 p.m.