Scale and Manipulate a Matrix — scale

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).

Author

Dongqiang Zeng

Examples

eset_gse62254 <- load_data("eset_gse62254")
#> ℹ Trying mirror 1/4: <https://github.com>
#> ✔ Download complete: "eset_gse62254"
eset2 <- scale_matrix(eset_gse62254, log2matrix = FALSE, manipulate = TRUE)
#> ✔ Retained 54675 of 54675 features
#> ℹ Retained 54675 features after manipulation