Set unfiltered DEGs on the object

Usage

SetDEGs(object, deg_table, assay)

Arguments

object: A geneda object
deg_table: A data.frame of DESeq2-like results containing at least columns log2FoldChange and padj
assay: What to name the DEG slot

Value

Updated geneda object with DEGs[[assay]] set

Examples

data(Snail1KO)
counts <- as.matrix(Snail1KO$rawCounts)
counts <- counts[rowSums(counts >= 10) >= 3, ]
meta <- Snail1KO$metadata
rownames(meta) <- meta$Sample
meta$Genotype <- factor(meta$Genotype, levels = c("WT", "Snai1_KO"))
norm <- log2(t(t(counts) / colSums(counts)) * 1e6 + 1)
obj <- GenEDA(normalized = norm, metadata = meta, counts = counts)

# Differential expression with DESeq2 (Snai1_KO vs WT)
dds <- DESeq2::DESeqDataSetFromMatrix(counts, meta, design = ~Genotype)
dds <- DESeq2::DESeq(dds, quiet = TRUE)
res <- as.data.frame(DESeq2::results(dds))
obj <- SetDEGs(obj, res, assay = "KO_vs_WT")
obj
#> geneda object
#>   features: 11247
#>   samples:  6
#>   HVGs: 0
#>   DimReduction: 0
#>   counts: present
#>   DEGs: KO_vs_WT