[DE DESeq2] Basic differential expression with DESeq2 #DE #DESeq2 #R

DE_DESeq2.R

library("tidyverse")
library("DESeq2")


# Create DESeq2 object:
dds <- DESeqDataSetFromMatrix(count_data,
                              colData = col_data,
                              design = ~ group)
# Run DE:
dds <- DESeq(dds)
res <- results(dds, contrast=c("group","1","2")) # group 1 compared to group 2

# Reformat:
res <- res %>% 
    as.data.frame() %>% 
    rownames_to_column("gene") %>% 
    arrange(padj) %>% 
    column_to_rownames("gene")