## ----knitr.setup, echo=FALSE--------------------------------------------------
library(knitr)
knitr::opts_chunk$set(
  echo = TRUE,
  warning=FALSE,
  message=FALSE,
  error = FALSE,
  tidy = FALSE,
  cache = TRUE)


# rmarkdown::render("loading_genesets.Rmd")

## ----load1, eval=FALSE--------------------------------------------------------
#  library(zenith)
#  
#  ## MSigDB as ENSEMBL genes
#  # all genesets in MSigDB
#  gs.msigdb = get_MSigDB()
#  
#  # only Hallmark gene sets
#  gs = get_MSigDB('H')
#  
#  # only C1
#  gs = get_MSigDB('C1')
#  
#  # C1 and C2
#  gs = get_MSigDB(c('C1', 'C2'))
#  
#  # C1 as gene SYMBOL
#  gs = get_MSigDB('C1', to="SYMBOL")
#  
#  # C1 as gene ENTREZ
#  gs = get_MSigDB('C1', to="ENTREZ")
#  
#  ## Gene Ontology
#  gs.go = get_GeneOntology()
#  
#  # load Biological Process and gene SYMBOL
#  gs.go = get_GeneOntology("BP", to="SYMBOL")

## ----load2, eval=FALSE--------------------------------------------------------
#  library(EnrichmentBrowser)
#  
#  # KEGG
#  gs.kegg = getGenesets(org = "hsa",
#                        db = "kegg",
#                        gene.id.type = "ENSEMBL",
#                        return.type = "GeneSetCollection")
#  
#  ## ENRICHR resource
#  # provides many additional gene set databases
#  df = showAvailableCollections( org = "hsa", db = "enrichr")
#  
#  head(df)
#  
#  # Allen_Brain_Atlas_10x_scRNA_2021
#  gs.allen = getGenesets( org = "hsa",
#                          db = "enrichr",
#                          lib = "Allen_Brain_Atlas_10x_scRNA_2021",
#                          gene.id.type = "ENSEMBL",
#                          return.type = "GeneSetCollection")

## ----custom, eval=FALSE-------------------------------------------------------
#  # Load gene sets from GMT file
#  gmt.file <- system.file("extdata/hsa_kegg_gs.gmt",
#                         package = "EnrichmentBrowser")
#  gs <- getGenesets(gmt.file)