phyloseq_coverage_raref: Coverage-based rarefaction

In vmikk/metagMisc: Miscellaneous functions for metagenomic analysis

Coverage-based rarefaction

Description

This function performs coverage-based rarefaction (interpolation) based on the analytical approach proposed by Chao and Jost (2012).

Usage

phyloseq_coverage_raref(
  physeq,
  coverage = NULL,
  iter = 1,
  replace = F,
  correct_singletons = FALSE,
  seeds = NULL,
  multithread = F,
  drop_lowcoverage = F,
  ...
)

Arguments

physeq	A phyloseq-class object
coverage	Numeric value for a particular sample coverage (between 0 and 1)
iter	Number of rarefication iterations
replace	Logical, whether to sample with replacement (TRUE) or without replacement (FALSE, default)
correct_singletons	Logical; if TRUE, singleton counts will be corrected with modified Good–Turing frequency formula (Chiu, Chao 2016)
seeds	Integer vector used for the reproducible random subsampling (should be of the same length as the number of iterations)
multithread	Logical or integer; if TRUE, attempts to run the function on multiple cores; integer defines the number of cores to use (if it is set to TRUE, all cores will be used)
drop_lowcoverage	Logical; if TRUE, samples with coverage lower than selected value will be removed (default, FALSE)
...	Additional arguments will be passed to rarefy_even_depth

Details

Samples standardized by size will have different degrees of completness. When we compare samples with the same coverage, we are making sure that samples are equally complete and that the unsampled species constitute the same proportion of the total individuals in each community (Chao, Jost, 2012).

Value

List of rarefied phyloseq-objects (or a single phyloseq object if iter = 1)

Examples

# Load data
data("esophagus")

# Coverage-based rarefaction
eso_raref <- phyloseq_coverage_raref(physeq = esophagus, iter = 1, coverage = 0.8)

# Perform coverage-based rarefaction multiple times (iter = 5)
eso_raref2 <- phyloseq_coverage_raref(physeq = esophagus, iter = 5, coverage = 0.8)

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