ALDEx2 ObjectThis method constructs a propr object from an
aldex.clr object. See Details.
aldex2propr(aldex.clr, how = "rho", select)An aldex.clr object.
A character string. The proportionality metric
used to build the propr object. Choose from
"rho", "phi", or "phs".
Optional. Use this to subset the final proportionality matrix without altering the result.
Returns a propr object.
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.