phyloseq_mult_raref_avg: Perform rarefaction and average relative OTU abundance

View source: R/phyloseq_mult_raref_avg.R

phyloseq_mult_raref_avgR Documentation

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 June 20, 2024, 7:20 a.m.