prune_groups: Prune group sizes

In alexpiper/taxreturn: An R package for retrieving and curating public DNA barcode reference data

Prune group sizes

Description

Prune group sizes

Usage

prune_groups(
  x,
  max_group_size = 5,
  dedup = TRUE,
  discardby = "length",
  prefer = NULL,
  quiet = FALSE
)

Arguments

x	A DNAbin or DNAStringset object
max_group_size	The maximum number of sequences with the same taxonomic annotation to keep
dedup	Whether sequences with identical taxonomic name and nucleotide bases sequences should be discarded first
discardby	How sequences from groups with size above max_group_size should be discarded. Options include "length" (Default) which will discard sequences from smallest to largest until the group is below max_group_size, "random" which will randomly pick sequences to discard until the group is below max_group_size.
prefer	A vector of sequence names that will be preferred when subsampling groups when discardby=random, or prefered when breaking ties in sequences of the same length when discardby=length. For instance high quality in-house sequences.
quiet	Whether progress should be printed to the console.

alexpiper/taxreturn documentation built on Sept. 14, 2024, 7:56 p.m.