## ----echo=FALSE----------------------------------------------------------
suppressPackageStartupMessages({
    library(DESeq2)
    library(airway)
    library(org.Hs.eg.db)
    library(limma)
})

## ----input---------------------------------------------------------------
library(DESeq2)
library(airway)
data(airway)
airway$dex <- relevel(airway$dex, "untrt")

## ----de------------------------------------------------------------------
des <- DESeqDataSet(airway, design = ~ cell + dex)
des <- DESeq(des)
res <- results(des)

## ----mapIds--------------------------------------------------------------
library(org.Hs.eg.db)
res$egid <- mapIds(
  org.Hs.eg.db, rownames(res), "ENTREZID", "ENSEMBL"
)

## ----trim----------------------------------------------------------------
table(is.na(res$padj), is.na(res$egid))
res <- subset(res, !is.na(padj) & !is.na(egid))
dim(res)

## ----goana---------------------------------------------------------------
library(limma)
go <- goana(res$egid[res$padj < .05], res$egid, "Hs")
go <- go[ order(go$P.DE), ]
t(go[1,])

## ----sanity--------------------------------------------------------------
head(subset(go, grepl("glucocorticoid", Term)), 3)

## ----term-id-mapping-----------------------------------------------------
map <- select(
  org.Hs.eg.db, res$egid, "GO", "ENTREZID"
)
head(map)