---
title: "Analyze with local GREAT"
author: "Zuguang Gu ( z.gu@dkfz.de )"
date: '`r Sys.Date()`'
output:
  html_document:
    toc: true
    toc_depth: 3
    toc_collapsed: false
    toc_float: true
vignette: >
  %\VignetteIndexEntry{2. Analyze with local GREAT}
  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteEncoding{UTF-8}
---

```{r, echo = FALSE, message = FALSE}
library(knitr)
knitr::opts_chunk$set(
    error = FALSE,
    tidy  = FALSE,
    message = FALSE,
    warning = FALSE,
    fig.align = "center")
```

**GREAT** ([Genomic Regions Enrichment of Annotations Tool](http://great.stanford.edu)) is a popular 
web-based tool to associate biological functions to genomic regions, however, its nature of being
an online tool has several limitations:

1. limited number of supported organisms. Current version 4.0.4 only supports four organisms: "hg38", "hg19", "mm10" and "mm9".
2. limited number of ontologies (or gene set collections). Current version 4.0.4 only supports seven ontologies (https://great-help.atlassian.net/wiki/spaces/GREAT/pages/655442/Version+History).
3. maximal 500,000 test regions (https://great-help.atlassian.net/wiki/spaces/GREAT/pages/655402/File+Size).
4. the update of annotation databases is only controlled by the GREAT developers.

From **rGREAT** version 1.99.0, it implements the GREAT algorithms locally and it can be seamlessly integrated
to the Bioconductor annotation ecosystem. This means, theoretically with **rGREAT**, it is possible to perform GREAT analysis
with any organism and with any type of gene set collection / ontology. Another advantage is, Bioconductor annotation packages
are always very well maintained and updated, which means the data source of your analysis can be ensured to be most up-to-date.

First let's load the **rGREAT** package and generate a random set of regions:

```{r}
library(rGREAT)

set.seed(123)
gr = randomRegions(nr = 1000, genome = "hg19")
```


## Perform local GREAT with `great()`

The function `great()` is the core function to perform local GREAT analysis. You can either use built-in annotations or use self-provided annotations.

### With defaultly supported annotation packages

`great()` has integrated many annotation databases which cover many organisms.
Users simply specify the name of gene set collection (via the second argument) and the source of TSS (via the third argument).

```{r}
res = great(gr, "MSigDB:H", "txdb:hg19")
res
```

There are following supported gene set collections. The first category are GO gene sets. The gene sets data is from **GO.db** package.

- `"GO:BP"`: Biological Process.
- `"GO:CC"`: Cellular Component.
- `"GO:MP"`: Molecular Function.

The prefix `GO:` can be omitted when it is specified in `great()`.

The second category of gene sets are from [MSigDB](https://www.gsea-msigdb.org/gsea/msigdb/). Note this is only for human. 
If you want to use MSigDB for other organisms, check vignette ["Work with other organisms"](other-organisms.html).

- `"msigdb:H"` Hallmark gene sets.
- `"msigdb:C1"` Positional gene sets.
- `"msigdb:C2"` Curated gene sets.
- `"msigdb:C2:CGP"` C2 subcategory: chemical and genetic perturbations gene sets. 
- `"msigdb:C2:CP"` C2 subcategory: canonical pathways gene sets. 
- `"msigdb:C2:CP:KEGG"` C2 subcategory: KEGG subset of CP.
- `"msigdb:C2:CP:PID"` C2 subcategory: PID subset of CP.
- `"msigdb:C2:CP:REACTOME"` C2 subcategory: REACTOME subset of CP.
- `"msigdb:C2:CP:WIKIPATHWAYS"` C2 subcategory: WIKIPATHWAYS subset of CP.
- `"msigdb:C3"` Regulatory target gene sets.
- `"msigdb:C3:MIR:MIRDB"` miRDB of microRNA targets gene sets.
- `"msigdb:C3:MIR:MIR_LEGACY"` MIR_Legacy of MIRDB.
- `"msigdb:C3:TFT:GTRD"` GTRD transcription factor targets gene sets.
- `"msigdb:C3:TFT:TFT_LEGACY"` TFT_Legacy.
- `"msigdb:C4"` Computational gene sets.
- `"msigdb:C4:CGN"` C4 subcategory: cancer gene neighborhoods gene sets.
- `"msigdb:C4:CM"` C4 subcategory: cancer modules gene sets.
- `"msigdb:C5"` Ontology gene sets.
- `"msigdb:C5:GO:BP"` C5 subcategory: BP subset.
- `"msigdb:C5:GO:CC"` C5 subcategory: CC subset.
- `"msigdb:C5:GO:MF"` C5 subcategory: MF subset.
- `"msigdb:C5:HPO"` C5 subcategory: human phenotype ontology gene sets.
- `"msigdb:C6"` Oncogenic signature gene sets.
- `"msigdb:C7"` Immunologic signature gene sets.
- `"msigdb:C7:IMMUNESIGDB"` ImmuneSigDB subset of C7.
- `"msigdb:C7:VAX"` C7 subcategory: vaccine response gene sets.
- `"msigdb:C8"` Cell type signature gene sets.

The prefix `msigdb:` can be omitted when specified in `great()` and the name of a MSigDB can be used as case insensitive.

**rGREAT** supports TSS from several sources. The value of argument `tss_source` should be encoded in a special format:

- Name of a `TxDb.*` package, e.g. `TxDb.Hsapiens.UCSC.hg19.knownGene`. Supported packages are in `rGREAT:::BIOC_ANNO_PKGS$txdb`.
- Genome version of the organism, e.g. "hg19". Then the corresponding TxDb package will be used.
- In a format of `RefSeq:$genome` where `$genome` is the genome version of an organism. RefSeqSelect genes (directly retrieved from UCSC database) will be used.
- In a format of `RefSeqCurated:$genome` where `$genome` is the genome version of an organism. RefSeqCurated subset (directly retrieved from UCSC database) will be used.
- In a format of `RefSeqSelect:$genome` where `$genome` is the genome version of an organism. RefSeqSelect subset (directly retrieved from UCSC database) will be used.
- In a format of `Gencode_v$version` where `$version` is Gencode version, such as 19 (for human) or M21 for mouse. Gencode protein coding genes will be used.
- In a format of `GREAT:$genome`, where `$genome` can only be "mm9", "mm10", "hg19", "hg38". TSS from GREAT will be used. The data is downloaded from https://great-help.atlassian.net/wiki/spaces/GREAT/pages/655445/Genes.

The difference of `RefSeqCurated` and `RefSeqSelect` is explained in https://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg38&g=refSeqComposite.

Some examples are:

```{r, eval = FALSE}
great(gr, "GO:BP", "hg19")
great(gr, "GO:BP", "TxDb.Hsapiens.UCSC.hg19.knownGene")
great(gr, "GO:BP", "RefSeq:hg19")
great(gr, "GO:BP", "GREAT:hg19")
great(gr, "GO:BP", "Gencode_v19")
```


### Manually set gene sets

If users have their own gene sets, the gene sets can be set as a named list of vectors where each vector corresponds to one gene set.
Please note the genes in the gene sets **must be mostly in Entrez ID type** (Default TSSs are from TxDb packages and most TxDb packages use Entrez ID
as primary ID, you can check the variable `rGREAT:::BIOC_ANNO_PKGS` to see the gene ID types in each TxDb package). In the following example, we use a gene set collection from [DSigDB](http://dsigdb.tanlab.org/DSigDBv1.0/collection.html).
This collection (FDA approved kinase inhibitors) only contains 28 gene sets.

Here `read_gmt()` is a simple function that reads a gmt file as a list of vectors, also performs gene ID conversion.


```{r}
gs = read_gmt(url("http://dsigdb.tanlab.org/Downloads/D2_LINCS.gmt"), 
    from = "SYMBOL", to = "ENTREZ", orgdb = "org.Hs.eg.db")
gs[1:2]
great(gr, gs, "hg19")
```

### Manually set TSS

Users may have their own set of genes/TSS, as in the following example:

```{r}
df = read.table(url("https://jokergoo.github.io/rGREAT_suppl/data/GREATv4.genes.hg19.tsv"))
# note there must be a 'gene_id' column
tss = GRanges(seqnames = df[, 2], ranges = IRanges(df[, 3], df[, 3]), 
    strand = df[, 4], gene_id = df[, 5])
head(tss)
```

In this case, users must manually generate an "extended TSS" by `extendTSS()` function. They should also explicitly specify the gene ID type
in `extendTSS()` so that `great()` can correctly map to the genes in gene sets.

In the example, IDs for genes in `tss` are symbols, thus, `gene_id_type` must be set to `"SYMBOL"` so that the correct gene ID type
will be selected for internal gene sets.

```{r}
et = extendTSS(tss, genome = "hg19", gene_id_type = "SYMBOL")
great(gr, "msigdb:h", extended_tss = et)
```

If gene ID type in `tss` is one of Ensembl/RefSeq/Entrez ID, `gene_id_type` argument can be omitted because the ID type can be automatically
inferred from the format of the gene IDs, but it is always a good idea to explicitly specify it if the data is self-provided.

### Manually set gene sets and TSS annotations

If your organism is not defaultly supported, you can always use the `extendTSS()` to manually construct one. Note in GREAT algorithm, TSS are first
extended by a rule (e.g. basal plus extension). `extendTSS()` accepts a `GRanges` object of gene or TSS and it returns a new `GRanges` object of extended TSS.

In the following example, since I don't have data for the organism not defaultly supported by **rGREAT**. I simply use human data to demonstrate
how to manually construct the extended TSS.


There are two objects for `extendTSS()`: the gene (or the TSS) and the length of chromosomes. The gene object must have a meta column named "gene_id" which stores
gene ID in a specific type (this ID type will be mapped to the genes in gene sets). The chromosome length object is a named vector. It controls the set of chromosomes to be used in the analysis and the border of chromosomes when extending TSSs.

```{r}
library(TxDb.Hsapiens.UCSC.hg19.knownGene)
gene = genes(TxDb.Hsapiens.UCSC.hg19.knownGene)
gene = gene[seqnames(gene) %in% paste0("chr", c(1:22, "X", "Y"))]
head(gene)
gl = seqlengths(gene)[paste0("chr", c(1:22, "X", "Y"))]  # restrict to normal chromosomes
head(gl)
```

Simply send `gene` and `gl` to `extendTSS()`:

```{r}
et = extendTSS(gene, gl)
head(et)
```

We can also manually construct the gene sets object, which is simply a named list of vectors where each vector contains genes in a gene set.
Here we directly use the object `gs` generated before which is a gene set collection from DSigDB.

<p style='color:red'>Please note again, gene IDs in `gs` (the gene sets) should be the same as in `et` (the extended TSSs).</p>

Now `gs` and `et` can be sent to `great()` to perform local GREAT with the annotation data you manually provided.

```{r}
great(gr, gene_sets = gs, extended_tss = et)
```

## Use BioMart genes and genesets

**rGREAT** also supports GO gene sets for a huge number of organisms retrieved from [Ensembl BioMart](https://www.ensembl.org/info/data/biomart/index.html).
A specific organism can be set with the `biomart_dataset` argument:


```{r, echo = FALSE}
if(!requireNamespace("BioMartGOGeneSets", quietly = TRUE)) {
    suppressMessages(BiocManager::install("jokergoo/BioMartGOGeneSets", update = FALSE))
}
```

```{r}
# Giant panda
gr_panda = randomRegionsFromBioMartGenome("amelanoleuca_gene_ensembl")
great(gr_panda, "GO:BP", biomart_dataset = "amelanoleuca_gene_ensembl")
```

Note both TSS and gene sets are from BioMart. The value for gene sets (the second argument) can only be one of `"GO:BP"`, `"GO:CC"` and `"GO:MF"`.

**rGREAT** now supports more than 600 organisms. The complete list can be found with `BioMartGOGeneSets::supportedOrganisms()`.

For non-model organisms, the default chromosomes may include many small contigs. You can set the `background` argument to a vector of chromosomes that you want to include.

## Set background regions

In the online GREAT tool, if background regions are set, [it actually uses a different test for the enrichment analysis](https://great-help.atlassian.net/wiki/spaces/GREAT/pages/655456/Statistics#Statistics-ExplicitBackgroundSet).
In GREAT, when background is set, input regions should be **exactly subset of background**. For example, let's say a background region list contains
five regions: `[1, 10], [15, 23], [34, 38], [40, 49], [54, 63]`, input regions can only be a subset of the five regions, which
means they can take `[15, 23], [40, 49]`, but it cannot take `[16, 20], [39, 51]`. In this setting, regions are taken
as single units and Fisher's exact test is applied for calculating the enrichment (by testing number of regions in the 2x2 contigency table).

This might be useful for certain cases, e.g., for a specific transcriptional
factor (TF), we take the union of ChIP-seq peaks of this TF from all tissues
as the background set, and only take peaks from one specific tisse as input
region set, and we want to test the enrichment of TF peaks in the tissue
compared to the "background". However, this "background definition" might not
be the case as many other users may think. They might take "background" as a
set of regions where they only want to perform GREAT (the Binomial method) in.
E.g. they may want to exclude "gap regions / unsequenced regions" from the
analysis because the null hypothesis of Binomial test is the input regions are
uniformly distributed in the genome. Since the unsequenced regions will never
be measured, they should be excluded from the analysis. Other examples are
that the background can be set as regions showing similar GC contents or CpG
density as the input regions.

`great()` supports two arguments `background` and `exclude` for setting a
proper background. If any one of the two is set, the input regions and the
extended TSS regions are intersected to the background, and GREAT algorithm is
only applied to the reduced regions.

When whole genome is set as background, denote $N_1$ as the total number of
input regions, $p_1$ as the fraction of genome that are overlapped to extended
TSS of genes in a certain gene set, and $K_1$ as the number of regions that
overlap to the gene set associated regions, then the enrichment test is based
on the random variable $K_1$ which follows Binomial distribution $K_1 \sim B(p_1, N_1)$.

Similarly, when background regions are set, denote $N_2$ as the total number
of input regions that <u>overlap to backgroud</u>, $p_2$ as <u>the fraction of
background</u> that are overlapped to extended TSS of genes in a certain gene
set, and $K_2$ as the number of regions that overlap to the gene set associated
regions <u>and also overlap to background</u>, then the enrichment test is based on
the random variable $K_2$ which follows Binomial distribution $K_2 \sim B(p_2, N_2)$.

In fact, the native hypergeometric method in GREAT can be approximated to the
binomial method here. Nevertheless, the binomial method is more general and it has
no restriction as the hypergeometric method where input regions must be
perfect subsets of backgrounds.

In the following example, `getGapFromUCSC()` can be used to retrieve gap regions from UCSC table browser.

```{r, eval = FALSE}
gap = getGapFromUCSC("hg19", paste0("chr", c(1:22, "X", "Y")))
great(gr, "MSigDB:H", "hg19", exclude = gap)
```

**Note as the same as online GREAT, rGREAT by default excludes gap regions from the analysis.**

Alternatively, `background` and `exclude` can also be set to a vector of chromosome names, then
the whole selected chromosomes will be included/excluded from the analysis.

```{r, eval = FALSE}
great(gr, "GO:BP", background = paste0("chr", 1:22))
great(gr, "GO:BP", exclude = c("chrX", "chrY"))
```

## Get enrichment table

Simply use `getEnrichmentTable()` function. 

```{r}
tb = getEnrichmentTable(res)
head(tb)
```

In `getEnrichmentTable()`, you can set argument `min_region_hits` to set
the minimal number of input regions that hit a geneset-associated regions.
Note the adjusted p-values will be recalculated in the table.

There are also columns for hypergeometric test on the numbers of genes, the same
as in the original GREAT method.

<p style='color:red'>There is a new column "mean_tss_dist" in the result table which is the mean absolute distance
of input regions to TSS of genes in a gene set. Please note with larger
distance to TSS, the more we need to be careful with the reliability of the
associations between input regions to genes.</p>

## Make volcano plot

In differential gene expression analysis, volcano plot is used to visualize relations between log2 fold change and (adjusted) p-values.
Similarly, we can also use volcano plot to visualize relations between fold enrichment and (adjusted) p-values for the enrichment analysis. 
The plot is made by the function `plotVolcano()`:

```{r, fig.width = 6, fig.height = 6}
plotVolcano(res)
```

As the enrichment analysis basically only looks for over-representations, it is actually half volcano.


## Get region-gene associations

`plotRegionGeneAssociations()` generates three plots similar as those by
online GREAT. `getRegionGeneAssociations()` returns a `GRanges` object containing
associations between regions and genes.

```{r, fig.width = 10, fig.height = 10/3, fig.align = 'center'}
plotRegionGeneAssociations(res)
getRegionGeneAssociations(res)
```

Being different from the online GREAT, `getRegionGeneAssociations()` on the local GREAT object calculates
the distance to TSS based on the borders of the input regions. The argument `by_middle_points` can 
be set to `TRUE` to let the distance be based on the middle points of input regions.

Please note the two meta columns are in formats of `CharacterList`
and `IntegerList` because a region may associate to multiple genes.


Of course you can set a specific geneset term by argument `term_id`.

```{r, fig.width = 10, fig.height = 10/3, fig.align = 'center'}
plotRegionGeneAssociations(res, term_id = "HALLMARK_APOPTOSIS")
getRegionGeneAssociations(res, term_id = "HALLMARK_APOPTOSIS")
```

## The Shiny application

`shinyReport()` creates a Shiny application to view the complete results:

```{r, eval = FALSE}
shinyReport(res)
```


## Session info

```{r}
sessionInfo()
```


