phyloseq_num_shared_otus: Estimate the number of shared and non-shared species...

In vmikk/metagMisc: Miscellaneous functions for metagenomic analysis

Estimate the number of shared and non-shared species (OTUs/ESvs) between all pairwise comparisons of samples.

Description

This function counts the number of OTUs that are common (shared) and distinct (non-shared) between a pair of samples. All pairwise sample combinations are considered, and the output is stored as a matrix.

Usage

phyloseq_num_shared_otus(physeq, use_Matrix = TRUE)

Arguments

physeq	A phyloseq-class object
use_Matrix	Logical, use sparse matrix class to perform the analysis (default, TRUE)

Details

This function uses the sparse matrix class implemented in the package Matrix to improve computational speed and decrease memory footprint.

Value

The function's output is a list containing three matrices (rows and columns correspond to samples):

• "shared" - The number of shared OTUs between the samples

• "nonshared_total" - The number of non-shared OTUs between the samples. This matrix contains the total number of non-shared OTUs between the two samples. The matrix is symmetric, meaning that the values in the matrix are equal on both sides of the diagonal.

• "nonshared_asymmetric" - The number of non-shared OTUs between the samples. The matrix is asymmetric, with the upper and lower triangular parts of the matrix representing the number of unique OTUs present only in one of the two samples.

See Also

phyloseq_extract_shared_otus, phyloseq_extract_non_shared_otus

Examples

data(esophagus)

# Count number of shared and non-shared OTUs
ps <- phyloseq_num_shared_otus(esophagus)
ps

# The same, but using base-R matrix class (not recommended for large data)
ps <- phyloseq_num_shared_otus(esophagus, use_Matrix = FALSE)
ps

# To obtain a list of shared or non-shared OTUs between a pair of samples, use
phyloseq_extract_shared_otus(x = esophagus, samp_names = c("B", "C"))
phyloseq_extract_non_shared_otus(x = esophagus, samp_names = c("B", "C"))

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