calcCoverage: Calculate sample coverage

In alakazam: Immunoglobulin Clonal Lineage and Diversity Analysis

Calculate sample coverage

Description

calcCoverage calculates the sample coverage estimate, a measure of sample completeness, for varying orders using the method of Chao et al, 2015, falling back to the Chao1 method in the first order case.

Usage

calcCoverage(x, r = 1)

Arguments

x	numeric vector of abundance counts.
r	coverage order to calculate.

Value

The sample coverage of the given order r.

References

1. Chao A. Nonparametric Estimation of the Number of Classes in a Population. Scand J Stat. 1984 11, 265270.

2. Chao A, et al. Unveiling the species-rank abundance distribution by generalizing the Good-Turing sample coverage theory. Ecology. 2015 96, 11891201.

See Also

Used by alphaDiversity.

Examples

# Calculate clone sizes
clones <- countClones(ExampleDb, groups="sample_id")

# Calculate 1first order coverage for a single sample
calcCoverage(clones$seq_count[clones$sample_id == "+7d"])

alakazam documentation built on Sept. 30, 2023, 9:07 a.m.