safeColScale: Safe Centering and Scaling of Columns
In PhilBoileau/scPCA: Sparse Contrastive Principal Component Analysis

safeColScale

R Documentation

Safe Centering and Scaling of Columns

Description

safeColScale is a safe utility for centering and scaling an input matrix X. It is intended to avoid the drawback of using scale on data with constant variance by inducing adding a small perturbation to truncate the values in such columns. It also takes the opportunity to be faster than scale through relying on matrixStats or DelayedMatrixStats, depending on the type of matrix being processed, for a key internal computation.

Usage

safeColScale(
  X,
  center = TRUE,
  scale = TRUE,
  tol = .Machine$double.eps,
  eps = 0.01,
  scaled_matrix = FALSE
)

Arguments

`X`	An input `matrix` to be centered and/or scaled. If `X` is not of class `matrix` or `DelayedMatrix`, then it must be coercible to a `matrix`.
`center`	A `logical` indicating whether to re-center the columns of the input `X`.
`scale`	A `logical` indicating whether to re-scale the columns of the input `X`.
`tol`	A tolerance level for the lowest column variance (or standard deviation) value to be tolerated when scaling is desired. The default is set to `double.eps` of machine precision `.Machine`.
`eps`	The desired lower bound of the estimated variance for a given column. When the lowest estimate falls below `tol`, it is truncated to the value specified in this argument. The default is 0.01.
`scaled_matrix`	A `logical` indicating whether to output a `ScaledMatrix` object. The centering and scaling procedure is delayed until later, permitting more efficient matrix multiplication and row or column sums downstream. However, this comes at the at the cost of numerical precision. Defaults to `FALSE`.