---
title: "Loading gene sets"
author:
- name: "[Gabriel Hoffman](http://gabrielhoffman.github.io)"
  affiliation: | 
    Icahn School of Medicine at Mount Sinai, New York
vignette: >
  %\VignetteIndexEntry{Example usage of zenith on GEUVAIDIS RNA-seq}
  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteEncoding{UTF-8}
  %\usepackage[utf8]{inputenc}
output:
  html_document:
    toc: true
    toc_float: true
---


```{r 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")
```

The `zenith` package builds on [EnrichmentBrowser](https://bioconductor.org/packages/EnrichmentBrowser/) to provde access to a range of gene set databases.  Genesets can take ~1 min to download and load the first time.  They are automatically cached on disk, so loading the second time takes just a second.  

# Easy loading of gene set databases
Here are some shortcuts to load common databases:  

```{r 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")
```



# Other databases
 [EnrichmentBrowser](https://bioconductor.org/packages/EnrichmentBrowser/) provides additional databases (i.e. [KEGG](https://www.genome.jp/kegg/), [Enrichr](https://maayanlab.cloud/Enrichr/#libraries)), alternate gene identifiers (i.e. ENSEMBL, ENTREZ) or species (i.e. hsa, mmu)

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