geneda S4 class — geneda-class • RGenEDA

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.

Examples

data(Snail1KO)
counts <- as.matrix(Snail1KO$rawCounts)
counts <- counts[rowSums(counts >= 10) >= 3, ]
meta <- Snail1KO$metadata
rownames(meta) <- meta$Sample
norm <- log2(t(t(counts) / colSums(counts)) * 1e6 + 1)
obj <- GenEDA(normalized = norm, metadata = meta, counts = counts)
is(obj, "geneda")
#> [1] TRUE