This function finds the reference that is most proportional to the geometric mean of the samples. Using this reference for an alr-transformation will permit an analysis that resembles that of a clr-transformation, but arguably with greater interpretability.
getReference(counts, alpha = NA)A data.frame or matrix. A "count matrix" with subjects as rows and features as columns. Note that this matrix does not necessarily have to contain counts.
A double. See vignette for details. Leave missing to skip Box-Cox transformation.
A reference as a character or integer.