HyperGResultBase-class {Category} | R Documentation |
This VIRTUAL class represents common elements of the return values
of generic functions like hyperGTest
.
A virtual Class: No objects may be created from it.
annotation
:"character"
giving the name of the annotation data package used. geneIds
:"ANY"
(usually
a character vector, but sometimes an integer vector).
The input vector of gene identifiers intersected with the
universe of gene identifiers used in the computation. testName
:"character"
identifying the testing method used.
pvalueCutoff
:show
method to
count number of significant terms. testDirection
:"over"
) or
underrepresentation("under"
).
signature(object =
"HyperGResultBase")
: return the name
of the annotation data package used. signature(r =
"HyperGResultBase")
: return the input
vector of gene identifiers intersected with the universe of
gene identifiers used in the computation. signature(r =
"HyperGResultBase")
: return the size of
the selected gene set used in the computation. This is simply
the length(geneIds(obj))
.signature(r =
"HyperGResultBase")
: accessor for the
pvalueCutoff
slot. signature(r =
"HyperGResultBase")
: accessor for the
testDirection
slot. Contains a string indicating
whether the test was for "over"
or "under"
representation of the categories.signature(object = "HyperGResultBase")
: return a character
string description of the test result. signature(object =
"HyperGResultBase")
: display an instance. signature(r =
"HyperGResultBase")
: return a string
describing the testing method used.isConditional(r)
TRUE
if the
result was obtained using a conditional algorithm.signature(r = "HyperGResultBase")
: Returns
a data.frame
summarizing the test result. Optional
arguments pvalue
and categorySize
allow
specification of maximum p-value and minimum cateogyrSize,
respectively.signature(r = "HyperGResultBase")
:
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.
Seth Falcon
HyperGResult-class
GeneGoHyperGeoTestResult-class