get_ntaxa: Count number of unique taxa

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

Description

Count the number of unique taxa represented by cluster(s) or sequences in phylota table Use rnk to specify a taxonomic level to count. If NULL counts will be made to the lowest level reported on NCBI.

Usage

get_ntaxa(phylota, cid = NULL, sid = NULL, rnk = NULL,
  keep_higher = FALSE)

Arguments

phylota	Phylota object
cid	Cluster ID(s)
sid	Sequence ID(s)
rnk	Taxonomic rank
keep_higher	Keep higher taxonomic ranks?

Value

vector

See Also

Other tools-public: calc_mad, calc_wrdfrq, drop_by_rank, drop_clstrs, drop_sqs, get_clstr_slot, get_nsqs, 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('bromeliads')
# how many species are there?
(get_ntaxa(phylota = bromeliads, cid = '0', rnk = 'species'))
# how many genera are there?
(get_ntaxa(phylota = bromeliads, cid = '0', rnk = 'genus'))
# how many families are there?
(get_ntaxa(phylota = bromeliads, cid = '0', rnk = 'family'))
# use list_ncbi_ranks() to see available rank names
(list_ncbi_ranks())

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