calc_mad: Calculate MAD score

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

Calculate MAD score

Description

For all sequences in a cluster(s) the MAD score.

Usage

calc_mad(phylota, cid)

Arguments

phylota	Phylota object
cid	Cluster ID(s)

Details

MAD is a measure of the deviation in sequence length of a cluster. Values range from 0 to 1. Clusters with values close to 1 have sequences with similar lengths.

Value

vector

See Also

Other tools-public: 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(), 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")
random_cids <- sample(bromeliads@cids, 10)
(calc_mad(phylota = bromeliads, cid = random_cids))

ropensci/phylotaR documentation built on July 9, 2023, 3:17 p.m.