cond_log2_transform_matrix: Apply log2 transformation on a matrix.

In pinin4fjords/shinyngs: Shiny apps for NGS data

Apply log2 transformation on a matrix.

Description

Apply log2 transformation on a matrix.

Usage

cond_log2_transform_matrix(
  matrix_data,
  should_transform = NULL,
  threshold = 30,
  rmzeros = FALSE,
  small_value = 1,
  reverse = FALSE
)

Arguments

matrix_data	A matrix containing data.
should_transform	A boolean indicating if the log2 transformation should be applied. If TRUE, log2 transformation is applied unconditionally. If FALSE, no transformation is applied. If NULL, a conditional transformation based on threshold is applied.
threshold	A numeric threshold to determine if the matrix should be log-transformed. This is only checked if should_transform is NULL.
rmzeros	A boolean indicating whether to remove zeros from the matrix. If TRUE, zeros are removed. Default is FALSE.
small_value	A small value to add to zero entries before log transformation.
reverse	Boolean, should we unlog rather than log?

Value

A modified matrix.

Examples

# Create a sample matrix
mat <- matrix(c(10, 0, 30, 0, 50, 60), ncol = 2)

# Use the function with different parameters
transformed_mat1 <- cond_log2_transform_matrix(mat, should_transform = TRUE)
transformed_mat2 <- cond_log2_transform_matrix(mat, should_transform = NULL, threshold = 40)
transformed_mat3 <- cond_log2_transform_matrix(mat, rmzeros = TRUE)

pinin4fjords/shinyngs documentation built on Jan. 18, 2025, 7:09 p.m.