drop_sqs: Drop sequences in a cluster

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

Drop sequences in a cluster

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

ropensci/phylotaR documentation built on July 21, 2024, 1:01 a.m.