ALDEx2 ObjectThis method constructs a propr object from an
aldex.clr object. See Details.
aldex2propr(aldex.clr, how = "perb", select)An aldex.clr object.
A character string. The proportionality method
used to build the propr object. For example,
"perb" returns an estimation of rho while "phit" returns
an estimation of phi.
See proportionality.
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.