GOHyperGResult-class {GOstats} | R Documentation |
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.
Objects can be created by calls of the form new("GOHyperGResult", ...)
.
goDag
:"graph"
representing
the DAG of GO terms tested.pvalue.order
:"integer"
.
The sort order of the computed p-values.annotation
:"character"
. The
name of the annotation data package used in the analysis.geneIds
:"ANY"
. The
intersection of the gene identifiers given as input and the
computed gene universe.testName
:"character"
.
Identifies the testing method used to produce this result instance.pvalueCutoff
:"numeric"
.
The cutoff for significance used for some testing methods.
Also used for pretty display in the show
method.
Class "HyperGResultBase"
, directly.
signature(r =
"GOHyperGResult")
: return an "integer"
vector: for each category term tested, the number of genes from
the gene set that are annotated at the term.signature(r = "GOHyperGResult")
:
return the graph
instance representing the DAG of the
GO terms that were tested.signature(r =
"GOHyperGResult")
: return a "numeric"
vector: the ordered p-values for each category term tested.signature(r =
"GOHyperGResult")
: return a "numeric"
vector: the odds ratio for each category term tested.signature(r =
"GOHyperGResult")
: return a "numeric"
vector: the expected number of genes for each GO term tested.signature(r =
"GOHyperGResult")
: return an "integer"
vector: for each category term tested, the number of genes from
the gene universe that are annotated at the term.signature(r =
"GOHyperGResult")
: return an "integer"
vector of length one giving the size of the gene universe set. signature(r =
"GOHyperGResult")
: return a list named by the
tested GO terms. Each element of the list is a vector of gene
identifiers (from the gene universe) annotated at the
corresponding GO term.signature(r =
"GOHyperGResult")
: return a list named by the
tested GO terms. Each element of the list is a vector of the
remaining gene identifiers (from the gene universe) annotated at
the corresponding GO term after the identifiers from significant
children were removed. This is only available when the
calculation performed used the conditional Hypergeometric
algorithm.signature(r = "GOHyperGResult")
: Returns a
data.frame
summarizing the test result. Optional
arguments pvalue
and categorySize
allow
specification of maximum p-value and minimum cateogyrSize,
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"
).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.signature(object = "GOHyperGResult")
:
Return a string giving a one-line description of the result.signature(r = "GOHyperGResult")
:
Return a TRUE
if the result was created using a
conditional algorithm and FALSE
otherwise.
Seth Falcon
GeneCategoryHyperGeoTestResult