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Suggest Rarefaction Depth

Source: R/rarefy.r
suggest_rarefy_depth.Rd

Calculates a rarefaction depth that balances retaining samples against retaining total observations.

Usage

suggest_rarefy_depth(biom)

Arguments

biom

An rbiom object, or any value accepted by as_rbiom().

Value

A single integer representing the suggested rarefaction depth.

Heuristic

This function selects a depth by analyzing the trade-off between dropping samples (to increase depth) and lowering depth (to keep samples).

  1. Calculate Yields: For every distinct sample depth in the dataset, calculate the total number of observations that would remain if the dataset were rarefied to that level. $$Yield_d = d \times N_{\ge d}$$ Where \(d\) is the depth and \(N_{\ge d}\) is the number of samples with at least that many reads.

  2. Define Threshold: Calculate 10% of the total observations in the original un-rarefied dataset.

  3. Select Depth: Find the lowest depth \(d\) where the \(Yield_d\) exceeds this 10% threshold.

This approach prioritizes keeping as many samples as possible, provided that doing so doesn't discard more than 90% of the dataset's total information.

See also

rarefy() which uses this heuristic when depth = NULL.

Examples

    library(rbiom)
    
    suggest_rarefy_depth(hmp50)
#> [1] 1183