## ----style, echo = FALSE, results = 'asis'-------------------------------
knitr::opts_chunk$set(
    eval=as.logical(Sys.getenv("KNITR_EVAL", "TRUE")),
    cache=as.logical(Sys.getenv("KNITR_CACHE", "TRUE"))
)
options(width = 75)


## ---- message=FALSE------------------------------------------------------
library(EnrichmentBrowser)


## ---- message = FALSE, echo = FALSE--------------------------------------
library(DESeq2)
library(airway)
library(dplyr)
library(org.Hs.eg.db)
library(GO.db)
library(limma)


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


## ------------------------------------------------------------------------
library(DESeq2)
des <- DESeqDataSet(airway, design = ~ cell + dex)
des <- DESeq(des)
res <- results(des)


## ------------------------------------------------------------------------
library(dplyr)
library(tibble)
tbl <- res %>%
    as.data.frame() %>%
    rownames_to_column("ENSEMBL") %>%
    as_tibble()
tbl


## ------------------------------------------------------------------------
library(org.Hs.eg.db)
tbl <- tbl %>%
    mutate(
        ENTREZID = mapIds(
            org.Hs.eg.db, ENSEMBL, "ENTREZID", "ENSEMBL"
        ) %>% unname()
    )
tbl


## ------------------------------------------------------------------------
tbl <- tbl %>%
    filter(!is.na(padj), !is.na(ENTREZID))
tbl


## ------------------------------------------------------------------------
library(limma)
go <-
    goana(tbl$ENTREZID[tbl$padj < .05], tbl$ENTREZID, "Hs") %>%
    as_tibble()


## ------------------------------------------------------------------------
library(GO.db)
go <-
    go %>%
    mutate(
        GOID = mapIds(
            GO.db, .$Term, "GOID", "TERM"
        ) %>% unname()
    ) %>%
    dplyr::select(GOID, everything()) %>%
    arrange(P.DE)


## ------------------------------------------------------------------------
go %>% filter(grepl("glucocorticoid", Term))


## ------------------------------------------------------------------------
genesets <-
    AnnotationDbi::select(org.Hs.eg.db, tbl$ENTREZID, "GO", "ENTREZID") %>%
    as_tibble() %>%
    dplyr::select(ENTREZID, GO, ONTOLOGY) %>%
    distinct()
genesets


## ------------------------------------------------------------------------
sessionInfo()