calculate_alr: Calculate ALR
In warrenmcg/sleuth-ALR: Compositional Approach to Sleuth Data Analysis

This function calculates the additive logratio transformation.

1 2	calculate_alr(mat, base = "e", denom_index = NULL, denom_method = "geomean")

`mat`	an D x M matrix of D target IDs and M samples
`base`	what should the base of the logarithm be? currently only supports base "e" and base 2.
`denom_index`	a character vector of target IDs or an integer vector of row numbers. If there is more than one, the geometric mean of the denominator values within one sample is used as the denominator.
`denom_method`	either 'geomean' or 'DESeq2' to use either the geometric mean of the features as the denominator, or the DESeq2-style size factors as the denominator. If there is only one feature, 'geomean' uses the feature's value itself, whereas 'DESeq2' will use the ratio of the feature to the geometric mean across samples.