drop_sqs: Drop sequences in a cluster

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

Description

Drop all sequences in a cluster except those identified by user.

Usage

drop_sqs(phylota, cid, sid)

Arguments

phylota	Phylota object
cid	Cluster ID
sid	Sequence ID(s) to be kept

Value

phylota

See Also

Other tools-public: calc_mad, calc_wrdfrq, drop_by_rank, drop_clstrs, get_clstr_slot, get_nsqs, get_ntaxa, get_sq_slot, 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("dragonflies")
# drop random sequences from cluster 0
clstr <- dragonflies[['0']]
# specify the sids to *keep*
sids <- sample(clstr@sids, 100)
(dragonflies <- drop_sqs(phylota = dragonflies, cid = '0', sid = sids))
# Note, sequences dropped may be represented in other clusters

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