is_txid_in_sq: Is txid in sequence?

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

Description

Checks if given txid is represented by sequence by looking at sequence source organism's lineage.

Usage

is_txid_in_sq(phylota, txid, sid)

Arguments

phylota	Phylota
txid	Taxonomic ID
sid	Sequence 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_clstr, 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)
sid <- tinamous@sids[[1]]
sq <- tinamous[[sid]]
txid <- sq@txid
# expect true
is_txid_in_sq(phylota = tinamous, txid = txid, sid = sid)

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