---
title: "An introduction to GSEABase"
author:
- name: "Martin Morgan"
  affiliation: 
  - Roswell Park Cancer Institute, Buffalo, NY
- name: "Paul Villafuerte"
  affiliation: "Vignette translation from Sweave to Rmarkdown / HTML"
package: | 
    GSEABase 1.61.0
    
    Report issues on https://github.com/Bioconductor/GSEABase/issues
abstract: >
  The `r Biocpkg('GSEABase')` package implements data structures and methods to
  represent, manipulate, and analyze gene sets in the context of gene set
  enrichment analysis. This includes construction of gene sets from
  reference resources, ID mapping, coloring according to phenotype
  association, and storing in gene set collections.
date: "`r format(Sys.time(), '%B %d, %Y')`"
vignette: >
  %\VignetteIndexEntry{An introduction to GSEABase}
  %\VignetteDepends{hgu95av2.db,GO.db, ReportingTools}
  %\VignetteKeywords{Gene Set Enrichment Analysis}
  %\VignettePackage{GSEABase}
  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteEncoding{UTF-8}
output:
  BiocStyle::html_document:
    number_sections: true
    toc: true
    toc_depth: 4
---

# GeneSet

```{r preliminaries, echo=FALSE}
## FIXME: <adjMat> adjacency matrix -- color w. +/- 1
## FIXME: limma topTable --> GeneColorSet
## w. verbose=TRUE
suppressPackageStartupMessages({
    library(GSEABase)
    library(hgu95av2.db)
    library(GO.db)
})
```

A `GeneSet` stores a set of related gene identifiers. Important components of
the gene set are a vector of identifiers, general descriptive information about
the set, and information about how the gene set was constructed. To construct a
gene set, use `GeneSet` . For example, to create a gene set from the
identifiers in a subset of the sample `ExpressionSet` in the
`r Biocpkg('Biobase')` package use

```{r GeneSet}
data(sample.ExpressionSet) # from Biobase
egs <- GeneSet(sample.ExpressionSet[201:250,], setName="Sample")
egs
```

Each gene set may have a name. The gene set contains `r length(geneIds(egs))`
identifiers ('genes') from the `ExpressionSet`. These are accessible using
`geneIds`, e.g.,

```{r geneIds}
head(geneIds(egs))
```

The gene set records that the identifiers are probeset names from the
annotation package `r Biocpkg('hgu95av2.db')`, and that the source of the gene
set was an `ExpressionSet`. Additional details are available:

```{r details}
details(egs)
```

The set identifier, set version, and creation date
provide mechanisms for carefully curating gene sets. Additional
information is automatically copied from the expression set used to
create `egs`.

```{r}
  ## FIXME: GeneSet(AnnotationIdentifier("hgu95av2")) --> non-empty
  ## FIXME: GeneSet(AnnotationIdentifier("hgu95av2"),
  ## collectionType=GOCollection()) filters on GOCollection (or KEGG)
```

View additional methods for creating gene sets with:

```{r GeneSet-methods}
showMethods("GeneSet", inherited=FALSE)
```

These are described on the `GeneSet` help page.

The identifier type of gene sets created from expression sets is `r as.character(class(geneIdType(egs)))`.
Additional predefined identifiers are available:

```{r GeneIdentifierTypes}
names(slot(getClass("GeneIdentifierType"), "subclasses"))
```

It is possible to map between identifier types
(provided the corresponding map in the annotation package exists):

```{r mapIdentifiers}
mapIdentifiers(egs, EntrezIdentifier())
```

`mapIdentifiers` consults the gene set to determine that annotation (probeset)
identifiers are to be converted to Entrez IDs based on the mapping in
the `r Biocpkg('hgu95av2.db')` package.
The function `mapIdentifiers` can automatically determine many of the common
maps; it is also possible to provide as a third argument an environment
containing an arbitrary map. Use the `verbose` argument of `mapIdentifiers` to be informed when the
map between identifier types is not 1:1.

A gene set can be created with different types of identifier, e.g., to
create a gene set with Entrez IDs, use

```{r GeneSet_Identifiers}
library(annotate)                       # getEG
eids <- unique(getEG(geneIds(egs), "hgu95av2"))
eids <- eids[!is.na(eids)]
GeneSet(EntrezIdentifier(), geneIds=as.character(eids))
```

The `collectionType` of a gene set provides additional information about a gene set.
Available collection types are

```{r CollectionType}
names(slot(getClass("CollectionType"), "subclasses"))
```

Collection types are most important when creating gene sets. For instance, the
`GOCollection` class allows creation of gene sets based on gene ontology (GO) terms.
The following command creates a gene set from two terms, including all
genes with a particular evidence code.

```{r GOCollection}
GeneSet(GOCollection(c("GO:0005488", "GO:0019825"),
                     evidenceCode="IDA"),
        geneIdType=EntrezIdentifier("org.Hs.eg.db"),
        setName="Sample GO Collection")

```

This creates a gene set by
consulting an object in the `r Biocpkg('GO.db')` package.
A gene set created from an expression set, and with collection type `GOCollection`
consults the appropriate environment in the annotation package associated
with the expression set.

Gene sets encoded in XML following the schema and conventions of the
Broad Institute can be read into _R_ as follows:

```{r Broad}
fl <- system.file("extdata", "Broad1.xml", package="GSEABase")
bgs <- GeneSet(BroadCollection(), urls=fl)
bgs
```

The example above uses a local file, but the source for the gene set
might also be a web address accessible via `http://` the protocol. The file name
is added to the url of the gene set. The set name and category of the
Broad collection indicate that the gene set contains gene symbols from
band 24 of the q arm of chromosome 16. The probe sets in chip `hgu95av2` 
corresponding to these symbols can be determined by mapping identifiers

```{r Broad-to-annotation}
bgs1 <- mapIdentifiers(bgs, AnnotationIdentifier("hgu95av2"))
bgs1
```

Subsetting creates sets with just the symbols identified. Subsetting can
use indices or symbol names.

```{r subset}
bgs[1:5]
bgs[c("GALNS", "LOC646365")]
```

Logical operations provide a convenient way to identify genes with
particular properties. For instance, the intersection

```{r egs-bgs}
egs & bgs1
```

is empty (note that the identifiers in the two sets were of
the same type), indicating that none of the identifiers in `egs` are on `16q24`.
Additional operations on sets include union (performed with `|`) and
difference (`setdiff`).

Methods exist to directly subset expression sets using gene sets

```{r subset-ExpressionSet}
sample.ExpressionSet[bgs,]
```

Remember that `sample.ExpressionSet` contains just `r nrow(sample.ExpressionSet)` probe sets, so the small size of the subset is not surprising. Note also that subsetting required mapping of symbol identifiers in `bgs` to `AnnotationIdentifiers`; this map used the annotation information in the expression set, and is not necessarily 1:1.

# GeneColorSet

A `GeneColorSet` is a gene set with "coloring" to indicate how features of genes and
phenotypes are associated. The following sample data describes how
changes in expression levels of several genes (with Entrez and Symbol
names) influence cisplatin resistance phenotype.

```{r GeneColorSet-setup, echo=FALSE, results="hide"}
conn <- textConnection("
Entrez ID, Gene Symbol, Expression level, Phenotype response
##used to be MRP2
1244, ABCC2, Increase, Resistant
538, ATP7A, Increase, Resistant
540, ATP7B, Increase, Resistant
9961, MVP, Increase, Resistant
##the LRP below must be MVP
##LRP, Increase, Resistant - need to know which one
7507,XPA, Increase, Resistant
2067, ERCC1, Increase, Resistant
##TOP, Increase, Resistant  - need to know which one, notes say II
672, BRCA1, Increase, Resistant
3725, JUN, Increase, Resistant
#GCS, Increase, Resistant  - my notes say alpha-GCS - so which one?
##I only found gamma at PubMed as being related
2730, GCLM, Increase, Resistant")
tbl <- read.csv(conn, strip.white=TRUE, comment.char="#", stringsAsFactors = TRUE)
close(conn)
unlink(conn)
```

```{r GeneColorSet-phenotype}
tbl
```

Note that three different aspects of data influence coloring: the phenotype
under consideration (cisplatin resistance), whether expression responses
refer to increasing or decreasing levels of gene expression, and whether
the phenotypic response represents greater resistance or sensitivity to
cisplatin. Here is the resulting gene color set:

```{r GeneColorSet-constructor}
gcs <- GeneColorSet(EntrezIdentifier(),
                    setName="A color set",
                    geneIds=as.character(tbl$Entrez.ID),
                    phenotype="Cisplatin resistance",
                    geneColor=tbl$Expression.level,
                    phenotypeColor=tbl$Phenotype.response)
gcs

```

Gene color sets can be used in the same way as gene sets, e.g., for subsetting
expression sets (provided the map between identifiers is 1:1, so that coloring
corresponding to identifiers can be determined). The `coloring` method allows
access to the coloring information with a data frame interface; `phenotype`,
`geneColor` and `phenotypeColor` provide additional accessors.

# GeneSetCollection

A `GeneSetCollection` is a collection of gene sets. Sets in the collection must
have distinct `setName`s, but can be a mix of `GeneSet` and GeneColorSet. Two
convenient ways to create a gene set collection are by specifying a source of
identifiers (e.g., an `ExpressionSet` or `AnnotationIdentifier`) and how the
identifiers are to be induced into sets (e.g., by consulting the GO or KEGG
ontologies):

```{r GeneSetCollection}
gsc <- GeneSetCollection(sample.ExpressionSet[201:250,], setType=GOCollection())
gsc
gsc[["GO:0005737"]]
```

In this example, the annotation identifiers of the sample expression set are
organized into gene sets based on their presence in GO pathways. Providing
arguments such as `evidenceCode` to `GOCollection` act to select just those
pathways satisfying the GO collection constraint:

```{r GeneSetCollection-GOCollection}
GeneSetCollection(sample.ExpressionSet[201:300,],
                  setType=GOCollection(evidenceCode="IMP"))
```

Sets in the collection are named after the GO terms, and can be accessed
by numeric index or name.

A file or url containing several gene sets defined by Broad XML can be
used to create a gene set collection, e.g.,

```{r GeneSetCollection-BroadCollection}
   ## FIXME: BroadCollection default to paste("c", 1:4, sep="")
   ## FIXME: GeneSetCollection(BroadCollection(), urls=fl); filters on bcCategory
fl <- system.file("extdata", "Broad.xml", package="GSEABase")
gss <- getBroadSets(fl)
gss
names(gss)
```

Identifiers within a gene set collection can be mapped to a common type
(provided maps are available) with, for example,

```{r mapIds-GeneSetCollection}
gsc <- mapIdentifiers(gsc, EntrezIdentifier())
gsc
gsc[["GO:0005737"]]
```

A convenient way to visualize a `GeneSetCollection` is with the
`r Biocpkg('ReportingTools')` package.

```{r ReportingTools, echo=TRUE}
## 'interesting' gene sets
idx <- sapply(gsc, function(x) length(geneIds(x))) > 2
  
library(ReportingTools)
gscReport <- HTMLReport(
    shortName="gsc_example",
    title="GSEABase Vignette GeneSetCollection",
    basePath=tempdir())
publish(gsc[idx], gscReport, annotation.db="org.Hs.eg")
url <- finish(gscReport)
```

The report can be viewed with

```{r ReportingTools-view, eval=FALSE}
browseURL(url)
```

This concludes a brief tour of gene sets and gene set collections
available in the `r Biocpkg('GSEABase')` package.