Prepare gene expression matrix

Prepares a gene expression matrix for GAM-clustering analysis. The function optionally converts gene identifiers to the annotation format used by the metabolic network, removes duplicates, retains the most highly expressed genes, and standardizes expression values. Biological replicates can be collapsed by averaging, and dimensionality reduction can be applied using PCA. The resulting matrix contains only processed features suitable for downstream network-based module discovery.

Usage

prepareData(
  E,
  gene.id.type = NULL,
  keep.top.genes = 12000,
  use.PCA = TRUE,
  use.PCA.n = 50,
  repeats = seq_len(ncol(E)),
  network.annotation
)

Arguments

E

Expression matrix with rownames as gene symbols.

gene.id.type

Gene ID type.

keep.top.genes

Which top of the most expressed genes to keep for the further analysis.

use.PCA

Whether to reduce matrix dimensionality by PCA or not.

repeats

Here you may collapse biological replicas by providing vector with repeated sample names

network.annotation

Metabolic network annotation.

Value

Expression matrix prepared for the analysis.