geneda S4 class

An S4 container for exploratory genomic data analysis. Stores optional raw counts, normalized data, sample metadata, highly variable genes (HVGs), and PCA dimensionality reduction results.

Slots

counts

Optional counts matrix (features x samples). Can be NULL.

normalized

Normalized expression matrix (features x samples).

metadata

Sample-level metadata data.frame (rows = samples).

HVGs

Character vector of selected highly variable gene IDs (row names).

DimReduction

List for PCA results with Scores, Eigenvectors, percent_var.

DEGs

List container for differential expression results.