ACMECalcSet-class {ACME} | R Documentation |
A subclass of ACMESet that can also store the parameters and results of an ACME calculation
Objects can be created by calls of the form new("ACMECalcSet",
assayData, phenoData, featureData, experimentData, annotation,
cutpoints, threshold, exprs, vals, ...)
. In addition to the
constraints defined by ACMESet, this class can also hold
the results (in the assayDataElement vals
) and the
threshold
and cutpoints
from an ACME do.aGFF.calc run
cutpoints
:Object of class "numeric"
The values
of the cutpoints used in an analysis by do.aGFF.calc, one per sample.
threshold
:Object of class "numeric"
The
threshold used in an analysis.
assayData
:Object of class "AssayData"
. See
ExpressionSet for details.
phenoData
:Object of class "AnnotatedDataFrame"
See
ExpressionSet for details.
featureData
:Object of class "AnnotatedDataFrame"
See
ExpressionSet for details.
experimentData
:Object of class "MIAME"
See
ExpressionSet for details.
annotation
:Object of class "character"
See
ExpressionSet for details.
.__classVersion__
:Object of class "Versions"
See
ExpressionSet for details.
Class "ACMESet"
, directly.
Class "ExpressionSet"
, by class "ACMESet", distance 2.
Class "eSet"
, by class "ACMESet", distance 3.
Class "VersionedBiobase"
, by class "ACMESet", distance 4.
Class "Versioned"
, by class "ACMESet", distance 5.
signature(x = "ACMECalcSet")
: A simple
getter for the cutpoints.
signature(x = "ACMECalcSet")
: A convenience
plotting method that also takes sample and chrom
signature(object = "ACMECalcSet")
: A show method
signature(x = "ACMECalcSet")
: A simple
getter for the threshold
signature(x = "ACMECalcSet")
: an accessor for the
p-values from a run of do.aGFF.calc. Returns a matrix with samples
in columns and probes in rows.
Sean Davis <sdavis2@mail.nih.gov>
showClass("ACMECalcSet") data(example.agff) b <- do.aGFF.calc(example.agff,thresh=0.95,window=1000) b head(vals(b)) threshold(b) cutpoints(b)