Convert methylation beta values to M-values

Applies the logit transform \(\log_2(\beta / (1 - \beta))\) after clipping betas away from 0 and 1. M-values are approximately homoscedastic and are the recommended scale for linear modeling and PCA of methylation data.

Usage

beta_to_m(beta, clip = 1e-04, drop_nonfinite = TRUE)

Arguments

beta: Numeric matrix of beta values (probes x samples), in [0, 1].
clip: Numeric: betas are clipped to [clip, 1 - clip] before the transform. Default 1e-4.
drop_nonfinite: Logical: drop probes (rows) with any missing/non-finite values after the transform. Default TRUE.

Value

A numeric matrix of M-values, probes x samples.

Examples

b <- matrix(runif(200, 0.01, 0.99), nrow = 20,
            dimnames = list(paste0("cg", 1:20), paste0("S", 1:10)))
m <- beta_to_m(b)
range(m)
#> [1] -6.061127  6.545274