Access DEGs container

Usage

DEGs(object, assay)

Arguments

object: A geneda object
assay: The name of the DEGs slot to return

Value

The DEG data.frame stored under assay, or NULL if it is not 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")
head(DEGs(obj, "KO_vs_WT"))
#>            baseMean log2FoldChange     lfcSE       stat       pvalue
#> TSPAN6    568.96042    -0.30768862 0.1375762 -2.2364967 2.531925e-02
#> DPM1     3024.10868     0.07165145 0.1055166  0.6790540 4.971037e-01
#> SCYL3      65.69871     0.28717973 0.2892136  0.9929675 3.207258e-01
#> C1orf112  404.59841    -0.27383316 0.1510443 -1.8129327 6.984220e-02
#> FUCA2    2665.61577    -0.06546739 0.1131406 -0.5786376 5.628337e-01
#> GCLC     2027.69197    -0.62464875 0.1255751 -4.9743045 6.548231e-07
#>                  padj
#> TSPAN6   6.309887e-02
#> DPM1     6.367775e-01
#> SCYL3    4.637427e-01
#> C1orf112 1.424725e-01
#> FUCA2    6.922724e-01
#> GCLC     5.985379e-06