raref_rtk: RTK-based rarefaction

In vmikk/metagMisc: Miscellaneous functions for metagenomic analysis

RTK-based rarefaction

Description

RTK-based rarefaction

Usage

raref_rtk(
  physeq,
  SampSize = NULL,
  MinSizeThreshold = NULL,
  iter = 1000,
  trimOTUs = TRUE,
  ...
)

Arguments

physeq	A phyloseq-class object
SampSize	Rarefaction depth (number of reads to sample)
MinSizeThreshold	Remove samples with number of reads less than this threshold
iter	Number of rarefication iterations
trimOTUs	Logical, if TRUE (default), OTUs that have a count of zero in every sample will be removed
...	Additional arguments will be passed to rtk

Value

List of rarefied phyloseq-objects.

Examples

data("esophagus")
eso_raref <- raref_rtk(esophagus, iter = 10)

# Benchmark
system.time( GPr <- raref_rtk(GlobalPatterns, SampSize = 5000, iter = 10, trimOTUs = T) )
system.time( GPr <- phyloseq_mult_raref(GlobalPatterns, SampSize = 5000, iter = 10, trimOTUs = T) )

vmikk/metagMisc documentation built on Feb. 14, 2024, 2:29 a.m.