phyloseq_coverage: Estimate the observed abundance-based sample coverage for...

In vmikk/metagMisc: Miscellaneous functions for metagenomic analysis

Estimate the observed abundance-based sample coverage for phyloseq object

Description

phyloseq_coverage estimates the sample completeness for the individual-based abundance data (number of sequencing reads) stored in 'phyloseq'-class objects.

Usage

phyloseq_coverage(physeq, correct_singletons = FALSE, add_attr = T)

Arguments

physeq	A phyloseq-class object
correct_singletons	Logical; if TRUE, singleton counts will be corrected with modified Good–Turing frequency formula (Chiu, Chao 2016)
add_attr	Logical; if TRUE, additional attributes (list of species abundances and singleton correction flag) will be added to the results

Details

Coverage represents a measure of sample completeness and is defined as the proportion of the total number of individuals in a community that belong to the species represented in the sample. Coverage complement (1 - Coverage) gives the proportion of the community belonging to unsampled species or the "coverage deficit" (Chao, Jost, 2012). Estimation of coverage is based on the number of singletons and doubletons in the sample.

Value

Data frame with coverage estimates for each sample

References

Chao A, Jost L. (2012) Coverage-based rarefaction and extrapolation: standardizing samples by completeness rather than size // Ecology 93(12): 2533–2547. DOI: 10.1890/11-1952.1

Examples

data("esophagus")
phyloseq_coverage(esophagus)

vmikk/metagMisc documentation built on June 20, 2024, 7:20 a.m.