Construct a geneda object

Usage

GenEDA(normalized, metadata, counts = NULL, DEGs = NULL)

Arguments

normalized: Normalized expression matrix (features x samples).
metadata: Sample metadata data.frame with row names matching colnames(normalized).
counts: Optional counts matrix (features x samples).
DEGs: Optional named list of DEG tables (data.frame or DESeqResults), stored with SetDEGs() using the list names as assay names. Each table needs log2FoldChange and padj columns.

Value

A geneda object.

Details

This constructor does not compute HVGs or PCA. Use FindVariableFeatures() and RunPCA() afterward.

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)
obj
#> geneda object
#>   features: 11247
#>   samples:  6
#>   HVGs: 0
#>   DimReduction: 0
#>   counts: present
#>   DEGs: none