Skip to contents

Calculate MAD score

Source: R/user-calc.R
calc_mad.Rd

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

Usage

calc_mad(phylota, cid)

Arguments

phylota

Phylota object

cid

Cluster ID(s)

Value

vector

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.

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))
#>      1061       577       911         7       207       296       551      1279 
#> 0.9604403 0.9975728 0.8632116 0.7303475 0.8608540 0.5875619 0.9845506 0.9688013 
#>        47      1217 
#> 0.6698142 0.9363895