Depth-robust alpha diversity residuals (McKnight / Mikryukov) — mcknight_residuals

Computes the residuals from a linear regression of \(\log(\text{richness})\) against \(\log(\text{sequencing depth})\) as a depth-robust alpha diversity metric (Mikryukov et al. 2023; McKnight et al. 2018, doi:10.5061/dryad.tn8qs35 ). This avoids discarding data through rarefaction.

Usage

mcknight_residuals_pq(physeq, add_to_sam_data = TRUE)

Arguments

physeq: (required) a phyloseq-class object obtained using the phyloseq package.
add_to_sam_data: (logical, default TRUE) if TRUE, a column mcknight_residuals is added to sample_data(physeq) and the augmented phyloseq object is returned. If FALSE, the numeric residuals vector is returned.

Value

Either a phyloseq object with an augmented sample_data (default) or a named numeric vector of residuals.

Author

Adrien Taudière

Examples

data_f_res <- mcknight_residuals_pq(data_fungi_mini)
head(sample_data(data_f_res)$mcknight_residuals)
#> [1]  0.3273090 -0.1430749  0.5681529  0.7310108 -0.7698491  0.4374109