phyloseq_mult_raref_avg: Perform rarefaction and average relative OTU abundance

In vmikk/metagMisc: Miscellaneous functions for metagenomic analysis

Perform rarefaction and average relative OTU abundance

Description

Perform rarefaction and average relative OTU abundance

Usage

phyloseq_mult_raref_avg(
  physeq,
  SampSize = NULL,
  iter = 1000,
  parallel = FALSE,
  verbose = TRUE,
  ...
)

Arguments

physeq	A phyloseq-class object
SampSize	Rarefaction depth (number of reads to sample)
iter	Number of rarefication iterations
parallel	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)
verbose	Logical; if TRUE, informational messages will be shown on screen
...	Additional arguments will be passed to phyloseq_mult_raref

Value

phyloseq object with relative OTU abundance averaged across multiple rarefactions.

Examples

# Load data
data(GlobalPatterns)

# Subset data for faster processing
GP <- prune_taxa(taxa_sums(GlobalPatterns) >= 100, GlobalPatterns)

# Perform multiple rarefaction and average relative OTU abundances across rarefaction iterations
res <- phyloseq_mult_raref_avg(GP)
res

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