This class represents the results of a test for overrepresentation
of GO categories among genes in a selected gene set based upon the
Hypergeometric distribution.
For details on extracting information from this object, be sure to
read the accessor documentation in the Category package:
HyperGResult-accessors.
Objects from the Class
Objects can be created by calls of the form new("GOHyperGResult", ...).
Slots
goDag:
Object of class "graph" representing
the DAG of GO terms tested.
pvalue.order:
Object of class "integer".
The sort order of the computed p-values.
annotation:
Object of class "character". The
name of the annotation data package used in the analysis.
geneIds:
Object of class "ANY". The
intersection of the gene identifiers given as input and the
computed gene universe.
testName:
Object of class "character".
Identifies the testing method used to produce this result instance.
pvalueCutoff:
Object of class "numeric".
The cutoff for significance used for some testing methods.
Also used for pretty display in the show method.
conditional:
A logical indicating whether the
calculation should condition on the GO structure.
testDirection:
A string which can be either "over"
or "under". This determines whether the test performed detects
over or under represented GO terms.
Extends
Class "HyperGResultBase", directly.
Methods
goDag
signature(r = "GOHyperGResult"):
return the graph instance representing the DAG of the
GO terms that were tested.
summary
signature(r = "GOHyperGResult"): Returns a
data.frame summarizing the test result. Optional
arguments pvalue and categorySize allow
specification of maximum p-value and minimum categorySize,
respectively. Optional argument htmlLinks is a logical
value indicating whether to add HTML links (useful in
conjunction with xtables print method with type set to
"html").
htmlReport
signature(r = "GOHyperGResult"): Write an
HTML version of the table produced by the summary method.
The path of a file to write the report to can be specified using
the file argument. The default is file="" which
will cause the report to be printed to the screen. If you wish
to create a single report comprising multiple results you can
set append=TRUE. The default is FALSE (overwrite
preexisting report file). You can specify a string to use as an
identifier for each table by providing a value for the
label argument. Additional named arguments will be
passed to the summary method.
description
signature(object = "GOHyperGResult"):
Return a string giving a one-line description of the result.