OBOCollection-class: Class "OBOCollection"

In Bioconductor/GSEABase: Gene set enrichment data structures and methods

Class "OBOCollection"

Description

OBOCollection extends the GOCollection class, and is usually constructed from a file formated following the OBO file format. See CollectionType for general use of collections with gene sets.

Objects from the Class

Objects are instantiated with calls to OBOCollection or getOBOCollection.

Slots

OBOCollection extends GOCollection and OBOCollection has the following additional slots (these slots are NOT meant to be manipulated directly by the user):

.stanza:

A data.frame representing the stanzas present in an OBO file. Row names of the data frame are unique stanza identifiers. The value column contains the stanza name (e.g., ‘Term’, i.e., the stanza name associated with a GO identifier).

.subset

A data.frame representing (optional) subsets defined in the collection. Subsets are defined in the header of an OBO file with a subsetdef tag. Row names of the data frame are the subsetdef names; the value column contains the subset definition.

.kv

A data.frame representing key-value pairs in the OBO source file. The row names of the data frame correspond to lines in the OBO file. The stanza_id column indexes the row of .stanza describing the stanza in which the key-value pair occured. The remaining columns (key, value) contain the parsed key and value.

Methods

OBOCollection has the following methods, in addition to those inherited from GOCollection.

These methods list and select subsets of OBOCollection:

subsets

signature(object="OBOCollection", display="named"): return a character vector of subsets present in object. Valid values for display are ‘named’ (a named character vector, with names equal to the names of the subsets and values the descriptions), ‘full’ (a character vector of name and description, with each pair formated into a single entry as “name (description)”), ‘key’ (subset names), or ‘value’ (subset descriptions).

[

signature(object="OBOCollection", i="character", j="missing", ...): return an OBOCollection by selecting just those subsets whose name matches the string(s) in i. This method calls the [,GOCollection method so, e.g., evidenceCode can be used to restricts which evidence codes the collection will identify.

These methods coerce to and from OBOCollection:

as

signature(object="OBOCollection", "graphNEL"): create a directed graph with nodes generated from ids(object) and edges from is_a relations of object.

as

signature(object="graphNEL", "OBOCollection"): create an OBOCollection with ids from the graph nodes, and edges from inNodes(object).

Author(s)

Martin Morgan <[e-mail]>

References

http://www.geneontology.org for details of the OBO format.

See Also

OBOCollection constructor; CollectionType classes.

Examples

fl <- system.file("extdata", "goslim_plant.obo", package="GSEABase")
obo <- getOBOCollection(fl)
obo
subsets(obo)
obo["goslim_plant", evidenceCode="TAS"]
g <- as(obo["goslim_goa"], "graphNEL")
if (interactive() && require("Rgraphviz")) {
    plot(g)
}

Bioconductor/GSEABase documentation built on Nov. 2, 2024, 6:35 a.m.