example_gen.R

library("pasilla")
library("DESeq2")

pasCts <- system.file("extdata",
                      "pasilla_gene_counts.tsv",
                      package="pasilla", mustWork=TRUE)
pasAnno <- system.file("extdata",
                       "pasilla_sample_annotation.csv",
                       package="pasilla", mustWork=TRUE)
cts <- as.matrix(read.csv(pasCts,sep="\t",row.names="gene_id"))
coldata <- read.csv(pasAnno, row.names=1)
coldata <- coldata[,c("condition","type")]
coldata$condition <- factor(coldata$condition)
coldata$type <- factor(coldata$type)
rownames(coldata) <- sub("fb", "", rownames(coldata))
cts <- cts[, rownames(coldata)]

dds <- DESeqDataSetFromMatrix(countData = cts,
                              colData = coldata,
                              design = ~ condition)
dds

featureData <- data.frame(gene=rownames(cts))
mcols(dds) <- DataFrame(mcols(dds), featureData)

keep <- rowSums(counts(dds)) >= 10
dds <- dds[keep,]

dds$condition <- factor(dds$condition, levels = c("untreated","treated"))

dds <- DESeq(dds)
res <- results(dds)
res

resultsNames(dds)

resLFC <- lfcShrink(dds, coef="condition_treated_vs_untreated", type="apeglm")