calc_mad: Calculate MAD score

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

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))

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