aldex2propr: Import 'ALDEx2' Object
In propr: Calculating Proportionality Between Vectors of Compositional Data

Description Usage Arguments Details Value

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

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

`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.

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.

Returns a propr object.

propr documentation built on Dec. 16, 2019, 9:30 a.m.