## ----setup, include = FALSE---------------------------------------------------
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

## ----install, eval = FALSE----------------------------------------------------
# if (!requireNamespace("BiocManager", quietly = TRUE)) {
#   install.packages("BiocManager")
# }
# 
# BiocManager::install("exploreSE")

## ----library------------------------------------------------------------------
library(exploreSE)

## ----quickstart, eval=FALSE---------------------------------------------------
# example(exploreSE, ask = FALSE)

## ----airway-dataset-----------------------------------------------------------
library(airway)
data(airway)
airway

## ----coldata_example----------------------------------------------------------
colData(airway)

## ----rowdata_example----------------------------------------------------------
rowData(airway)

## ----example_filtering--------------------------------------------------------
dim(airway)
airway <- airway[rowData(airway)$gene_biotype == "protein_coding", ]
dim(airway)

## ----example_adding_baseline--------------------------------------------------
library(DESeq2)
airway <- DESeqDataSet(airway, design = ~dex)
airway <- DESeq(airway)
baseline <- results(airway)

## ----example_adding_controlled------------------------------------------------
design(airway) <- ~ cell + dex
airway <- DESeq(airway)
cell_controlled <- results(airway)

## ----example_deedee-----------------------------------------------------------
library(DeeDeeExperiment)
airway <- DeeDeeExperiment(airway)
airway <- addDEA(airway, baseline)
airway <- addDEA(airway, cell_controlled)

## ----example_structure_showcase-----------------------------------------------
airway

## ----example_gos--------------------------------------------------------------
airway <- get.gos(obj = airway, NAME = "baseline", gene_type = "ENSEMBL")
airway <- get.gos(obj = airway, NAME = "cell_controlled", gene_type = "ENSEMBL")

## ----example_showcase_with_gos------------------------------------------------
airway

## ----running_the_app, eval=FALSE----------------------------------------------
# app <- exploreSE(object = airway)
# shiny::runApp(app, port = 1234)

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