R: Import 'ALDEx2' Object

aldex2propr {propr} | R Documentation

## Import `ALDEx2` Object

### Description

This method constructs a `propr` object from an `aldex.clr` object. See Details.

### Usage

    aldex2propr(aldex.clr, how = "rho", select)

### Arguments

`aldex.clr` | An `aldex.clr` object.
`how` | A character string. The proportionality metric used to build the `propr` object. Choose from "rho", "phi", or "phs".
`select` | Optional. Use this to subset the final proportionality matrix without altering the result.

### Details

The `ALDEx2` package has two exceptional features useful in proportionality analysis too. First, `ALDEx2` offers a number of extra log-ratio transformations, toggled by the `denom` argument in `aldex.clr`. Second, `ALDEx2` estimates per-feature technical variation within each sample using Monte-Carlo instances drawn from the Dirichlet distribution.

The `aldex2propr` function takes advantage of both of these features by constructing a `propr` object directly from an `aldex.clr` object. When interpreting the resultant `propr` object, keep in mind that `ALDEx2` adds 0.5 to all `@counts` regardless of whether the counts contain any zeros. Otherwise, the `@logratio` slot contains the log-ratio transformed counts as averaged across all Monte Carlo instances. Likewise, the `@matrix` slot gets filled with the proportionality matrix as averaged across all Monte Carlo instances.

The `select` argument subsets the feature matrix after log-ratio transformation but before calculating proportionality. This reduces the run-time and RAM overhead without impacting the final result. Removing lowly abundant features prior to log-ratio transformation could otherwise change the proportionality measure.

### Value

Returns a `propr` object.

[Package propr version 4.1.1 Index]