Scales a gene expression matrix, optionally applies logarithmic
transformation, and performs feature manipulation to remove problematic
variables (e.g., genes with zero variance or missing values).
Usage
scale_matrix(matrix, log2matrix = TRUE, manipulate = TRUE)
Arguments
- matrix
Numeric matrix with genes as rows and samples as columns.
- log2matrix
Logical indicating whether to apply log2 transformation
using [log2eset()]. Default is `TRUE`.
- manipulate
Logical indicating whether to perform feature manipulation
to remove problematic features. Default is `TRUE`.
Value
A scaled matrix (genes as rows, samples as columns).
Examples
eset_gse62254 <- load_data("eset_gse62254")
eset2 <- scale_matrix(eset_gse62254, log2matrix = FALSE, manipulate = TRUE)
#> ✔ Retained 54675 of 54675 features
#> ℹ Retained 54675 features after manipulation