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

## ----eval = FALSE-------------------------------------------------------------
#  if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager")
#  
#  BiocManager::install("scMultiome")
#  

## ----results = FALSE, message=FALSE-------------------------------------------
library(scMultiome)
listDatasets()

## ----results = 'asis', echo = FALSE-------------------------------------------
lds <- listDatasets()
knitr::kable(lds, caption = "Available Data Sets")


## -----------------------------------------------------------------------------
prostateENZ(metadata = TRUE)


## -----------------------------------------------------------------------------
tfBinding(genome = "hg38", source ="atlas", metadata = TRUE)

## ----devtoolsAvailable, eval = FALSE, include = FALSE-------------------------
#  devtoolsAvailable <- requireNamespace("devtools", quietly = TRUE)
#  
#  if (devtoolsAvailable) {
#      # attach development version of the package
#      devtools::load_all()
#  }
#  

## ----saving, class.output = "scroll250", class.echo = "scroll250"-------------
# construct a dummy data set
mae <- dummyMAE()
mae

# name the file to save to
fileName <- tempfile(fileext = ".h5")

# save data set
saveMAE(mae, fileName)


## ----test reloading-----------------------------------------------------------
testFile(fileName)


## ----making metadata, eval = FALSE--------------------------------------------
#  makeMakeMetadata(<DATASET_NAME>)

## ----build metadata, eval = FALSE---------------------------------------------
#  source(system.file("scripts", "make-metadata.R", package = "scMultiome"))

## ----validation, eval = FALSE, class.output = "scroll250"---------------------
#  ExperimentHubData::makeExperimentHubMetadata(dirname(system.file(package = "scMultiome")))

## ----making, eval = FALSE-----------------------------------------------------
#  makeMakeData(<DATASET_NAME>)
#  

## ----making2, eval = FALSE----------------------------------------------------
#  makeR("dataset")
#  

## ----documentation, eval = FALSE----------------------------------------------
#  # build documentation
#  devtools::document()
#  
#  # view package man page
#  ?scMultiome
#  
#  # view your data set man page
#  help("dataset")
#  

## ----DESCRIPTION, eval = FALSE------------------------------------------------
#  desc::desc_add_author("<GIVEN_NAME>", "<FAMILY_NAME>", "<EMAIL>", role = "aut")
#  desc::desc_bump_version("minor")
#  

## ----upload, eval = FALSE-----------------------------------------------------
#  uploadFile(file = fileName, sasToken = "<SAS_TOKEN>")
#  

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