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.
OBOCollection
or
getOBOCollection
.OBOCollection
extends GOCollection
and
OBOCollection
has the following additional slots (these slots are
NOT meant to be manipulated directly by the user):
.stanza
: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
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
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.OBOCollection
has the following methods, in addition to those inherited from
GOCollection
. These methods list and select subsets of OBOCollection
:
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.OBOCollection
:
signature(object="OBOCollection", "graphNEL")
:
create a directed graph with nodes generated from
ids(object)
and edges from is_a
relations of
object
.signature(object="graphNEL", "OBOCollection")
:
create an OBOCollection
with ids
from the graph
nodes, and edges from inNodes(object)
.OBOCollection
constructor;
CollectionType
classes.
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)
}
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