Applies a log-x transformation to matrix

Applies a log-x transformation (by default log2) through the log() function.

Usage

transform_logx(
  mat,
  return_matrix_only = FALSE,
  log_base = 2,
  pre_log_function = zero_to_half_min
)

Arguments

mat

Numeric matrix.

return_matrix_only

Logical, should only the transformed matrix be returned? If TRUE, the function will return a matrix. If FALSE, the function instead returns a list with the transformed data and potentially other information relevant to the transformation. Default value is FALSE.

log_base

Numeric, the base with respect to which logarithms are computed.

pre_log_function

Function that will be applied to the matrix before the log transformation (e.g. to apply an offset to the values to avoid issues with zeros). Default value is the zero_to_half_min() function.

Value

Depending on the return_matrix_only, either a matrix of transformed data, or a list with the following elements:

• transformed_data: matrix of the transformed data;

• info_transformation: a list with the log base used and the function applied prior to log-transformation.