import/export {GSEABase} | R Documentation

## Read and write gene sets from Broad or GMT formats

### Description

`getBroadSets` parses one or more XML files for gene sets. The file can reside locally or at a URL. The format followed is that defined by the Broad (below). `toBroadXML` creates Broad XML from `BroadCollection` gene sets.

`toGmt` converts `GeneSetColletion` objects to a character vector representing the gene set collection in GMT format. `getGmt` reads a GMT file or other character vector into a `GeneSetColletion`.

### Usage

    getBroadSets(uri, ..., membersId=c("MEMBERS_SYMBOLIZED", "MEMBERS_EZID"))
    toBroadXML(geneSet, con, ...)
    asBroadUri(name,
               base="http://www.broad.mit.edu/gsea/msigdb/cards")
    getGmt(con, geneIdType=NullIdentifier(),
           collectionType=NullCollection(), sep="\t", ...)
    toGmt(x, con, ...)

### Arguments

`uri` | A file name or URL containing gene sets encoded following the Broad specification. For Broad sets, the uri can point to a MSIGDB.
`geneSet` | A `GeneSet` with `collectionType` `BroadCollection` (to ensure that required information is available).
`x` | A `GeneSetCollection` or other object for which a `toGmt` method is defined.
`con` | A (optional, in the case of `toXxx`) file name or connection to receive output.
`name` | A character vector of Broad gene set names, e.g., `c('chr16q', 'GNF2_TNFSF10')`.
`base` | Base uri for finding Broad gene sets.
`geneIdType` | A constructor for the type of identifier the members of the gene sets represent. See `GeneIdentifierType` for more information.
`collectionType` | A constructor for the type of collection for the gene sets. See `CollectionType` for more information.
`sep` | The character string separating members of each gene set in the GMT file.
`...` | Further arguments passed to the underlying XML parser, particularly `file` used to specify an output `connection` for `toBroadXML`.
`membersId` | XML field name from which `geneIds` are derived. Choose one value; default “MEMBERS_SYMBOLIZED”.

### Value

`getBroadSets` returns a `GeneSetCollection` of gene sets.

`toBroadXML` returns a character vector of a single `GeneSet` or, if `con` is provided, writes the XML to a file.

`asBroadUri` can be used to create URI names (to be used by `getBroadSets` of Broad files.

`getGmt` returns a `GeneSetCollection` of gene sets.

`toGmt` returns character vectors where each line represents a gene set. If `con` is provided, the result is written to the specified connection.

### Note

Actual Broad XML files differ from the DTD (e.g., an implied ',' separator between genes in a set); we parse to and from files as they exists the actual files.

### Author(s)

Martin Morgan <mtmrogan@fhcrc.org>

### References

http://www.broad.mit.edu/gsea/

### See Also

`GeneSetCollection` `GeneSet`

### Examples

    ## 'fl' could also be a URI
    fl <- system.file("extdata", "Broad.xml", package="GSEABase")
    gss <- getBroadSets(fl) # GeneSetCollection of 2 sets
    names(gss)
    gss[[1]]

    ## Not run:
    ## Download 'msigdb_v2.5.xml' or 'c3.all.v2.5.symbols.gmt' from the
    ## Broad, http://www.broad.mit.edu/gsea/downloads.jsp#msigdb, then
    gsc <- getBroadSets("/path/to/msigdb_v.2.5.xml")
    types <- sapply(gsc, function(elt) bcCategory(collectionType(elt)))
    c3gsc1 <- gsc[types == "c3"]
    c3gsc2 <- getGmt("/path/to/c3.all.v2.5.symbols.gmt",
                     collectionType=BroadCollection(category="c3"),
                     geneIdType=SymbolIdentifier())

    ## End(Not run)

    fl <- tempfile()
    toBroadXML(gss[[1]], con=fl)
    noquote(readLines(fl))
    unlink(fl)

    ## Not run:
    toBroadXML(gss[[1]]) # character vector

    ## End(Not run)

    fl <- tempfile()
    toGmt(gss, fl)
    getGmt(fl)
    unlink(fl)

[Package GSEABase version 1.54.0 Index]