## ----message=FALSE, include=FALSE, results="hide", setup, echo=FALSE----------
knitr::opts_chunk$set(
  echo = TRUE,
  eval = TRUE,
  message = FALSE,
  warning = FALSE,
  collapse = TRUE,
  tidy = FALSE,
  cache = FALSE,
  dev = "png",
  comment = "#>"
)
library(rbioapi)
rba_options(timeout = 30, skip_error = TRUE)

## ----rba_mieaa_cats, eval=FALSE-----------------------------------------------
# ## A list of available enrichment categories for:
# 
# ## mature human miRNA:
# rba_mieaa_cats(mirna_type = "mature", species = 9606)
# 
# ## precursor human miRNA
# rba_mieaa_cats(mirna_type = "precursor", species = 9606)
# 
# ## precursor zebrafish miRNA
# rba_mieaa_cats(mirna_type = "mature", species = "Danio rerio")

## ----rba_mieaa_enrich, message=TRUE-------------------------------------------
## 1 We create a variable with our miRNAs' mature IDs
mirs <- c(
  "hsa-miR-20b-5p", "hsa-miR-144-5p", "hsa-miR-17-5p", "hsa-miR-20a-5p",
  "hsa-miR-222-3p", "hsa-miR-106a-5p", "hsa-miR-93-5p", "hsa-miR-126-3p",
  "hsa-miR-363-3p", "hsa-miR-302c-3p", "hsa-miR-374b-5p", "hsa-miR-18a-5p",
  "hsa-miR-548d-3p", "hsa-miR-135a-3p", "hsa-miR-558", "hsa-miR-130b-5p",
  "hsa-miR-148a-3p"
)

## 2a We can perform enrichment analysis on our miRNA set without limiting the analysis to any categories
mieaa_all <- rba_mieaa_enrich(
  test_set = mirs,
  mirna_type = "mature",
  test_type = "ORA",
  species = 9606
)

## 2b Or, We can limit the enrichment to certain datasets (enrichment categories)
mieaa_kegg <- rba_mieaa_enrich(
  test_set = mirs,
  mirna_type = "mature",
  test_type = "ORA",
  species = 9606,
  categories = "KEGG_mature"
)

## ----mieaa_kegg_table, echo=FALSE---------------------------------------------
if (is.data.frame(mieaa_kegg)) {
  DT::datatable(
    data = mieaa_kegg,
    options = list(
      scrollX = TRUE, 
      paging = TRUE,
      fixedHeader = TRUE,
      keys = TRUE,
      pageLength = 10
    )
  )
} else {
  print("Vignette building failed. It is probably because the web service was down during the building.")
}

## ----rba_meaa_submit/status/results, eval=FALSE-------------------------------
# ## 1 Submit enrichment request to miEAA
# request <- rba_mieaa_enrich_submit(
#   test_set = mirs,
#   mirna_type = "mature",
#   test_type = "ORA",
#   species = 9606,
#   categories = c("miRWalk_Diseases_mature", "miRWalk_Organs_mature")
# )
# 
# ## 2 check for job's running status
# rba_mieaa_enrich_status(job_id = request$job_id)
# 
# ## 3 If the job has completed, retrieve the results
# results <- rba_mieaa_enrich_results(job_id = request$job_id)

## ----sessionInfo, echo=FALSE--------------------------------------------------
sessionInfo()