cghExSet-class {Neve2006} | R Documentation |
combination of an ExpressionSet and CGH assay results
make_cghExSet(exprs, logRatios, cloneMeta, pd, mi, anno) # pd is AnnotatedDataFrame, mi is MIAME
exprs |
matrix of expression assay results |
logRatios |
matrix of aCGH assay results |
cloneMeta |
AnnotatedDataFrame for aCGH clone descriptions |
pd |
AnnotatedDataFrame for sample level data |
mi |
MIAME instance for experiment documentation |
anno |
character string with annotation platform descriptor for expression data |
Objects can be created by calls of the form new("cghExSet", phenoData, experimentData, annotation, exprs, logRatios, cloneMeta)
.
cghAssays
:"AssayData"
rectangular
representation of logRatio data from CGH cloneMeta
:"AnnotatedDataFrame"
information
on chromosome and offset of clonesassayData
:"AssayData"
expression assay results phenoData
:"AnnotatedDataFrame"
sample level data featureData
:"AnnotatedDataFrame"
reporter
level metadata for expression assay results experimentData
:"MIAME"
container for
experiment documentation annotation
:"character"
identifiers for
expression and CGH platforms, as a named vector with elements named 'exprs'
and 'logRatios' .__classVersion__
:"Versions"
Class eSet-class
, directly.
Class VersionedBiobase-class
, by class "eSet", distance 2.
Class Versioned-class
, by class "eSet", distance 3.
signature(cghSet = "cghExSet")
: extract annotated data
frame on clone locations for CGH component signature(cghSet = "cghExSet")
: extract character vector
of clone IDs for CGH component signature(object = "cghExSet")
: extract expression assay results signature(.Object = "cghExSet")
: infrastructure signature(cghSet = "cghExSet")
: extract CGH assay results signature(object = "cghExSet")
: display object in concise form V Carey <stvjc@channing.harvard.edu>
R. M. Neve Cancer Cell Dec 2006
showClass("cghExSet") data(neveExCGH) logRatios(neveExCGH)[1:4,] exprs(neveExCGH)[1:4,]