mclr | R Documentation |
Modified central log ratio (mclr) transformation
mclr(dat, base = exp(1), tol = 1e-16, eps = NULL, atleast = 1)
dat |
raw count data or compositional data (n by p) does not matter. |
base |
exp(1) for natural log |
tol |
tolerance for checking zeros |
eps |
epsilon in eq (2) of the paper "Yoon, Gaynanova, M\"uller (2019), Frontiers in Genetics". positive shifts to all non-zero compositions. Refer to the paper for more details. eps = absolute value of minimum of log ratio counts plus c. |
atleast |
default value is 1. Constant c which ensures all nonzero values to be strictly positive. default is 1. |
mclr
returns a data matrix of the same dimension with input data matrix.
data(QMP) RMP <- QMP/rowSums(QMP) mclr_RMP <- mclr(RMP)
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