aldex2propr: Import 'ALDEx2' Object

In tpq/propr: An R package to calculate proportionality and other measures for compositional data

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.

tpq/propr documentation built on April 21, 2024, 12:50 p.m.