is_txid_in_clstr: Is txid in cluster?

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

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)

phylotaR documentation built on May 1, 2019, 9:26 p.m.