Description Extends Creating Objects Slots Methods Author(s) See Also
Container for high-throughput assays and experimental
metadata. SnpSet
class is derived from
eSet
, and requires matrices call
,
callProbability
as assay data members.
Directly extends class eSet
.
new('SnpSet',
phenoData = [AnnotatedDataFrame],
experimentData = [MIAME],
annotation = [character],
protocolData = [AnnotatedDataFrame],
call = [matrix],
callProbability = [matrix],
...)
SnpSet
instances are usually created through
new("SnpSet", ...)
. Usually the arguments to new
include call
(a matrix of genotypic calls, with features (SNPs)
corresponding to rows and samples to columns), phenoData
,
experimentData
, annotation
, and protocolData
.
phenoData
, experimentData
, annotation
and
protocolData
can be missing, in which case they are assigned
default values.
Inherited from eSet
:
assayData
:Contains matrices with equal
dimensions, and with column number equal to
nrow(phenoData)
. assayData
must contain a matrix
call
with rows representing features (e.g., SNPs)
and columns representing samples, and a matrix
callProbability
describing the certainty of the
call. The content of call
and callProbability
are
not enforced by the class. Additional matrices of
identical size may also be included in
assayData
. Class:AssayData-class
phenoData
:See eSet
experimentData
:See eSet
annotation
:See eSet
protocolData
:See eSet
Class-specific methods:
snpCall(SnpSet)
, snpCall(SnpSet,matrix)<-
Access and
set elements named call
in the AssayData
slot.
exprs(SnpSet)
, exprs(SnpSet,matrix)<-
Synonym
for snpCall
.
snpCallProbability(SnpSet)
,
snpCallProbability<-(SnpSet,matrix)<-
Access and set
elements named callProbability
in the AssayData
slot.
Derived from eSet
:
updateObject(object, ..., verbose=FALSE)
Update instance to current version, if necessary. See updateObject
and eSet
isCurrent(object)
Determine whether version of object is current. See isCurrent
isVersioned(object)
Determine whether object contains a 'version' string describing its structure . See isVersioned
sampleNames(SnpSet)
and sampleNames(SnpSet)<-
:See eSet
featureNames(SnpSet)
, featureNames(SnpSet, value)<-
:See eSet
dims(SnpSet)
:See eSet
phenoData(SnpSet)
, phenoData(SnpSet,value)<-
:See eSet
varLabels(SnpSet)
, varLabels(SnpSet, value)<-
:See eSet
varMetadata(SnpSet)
, varMetadata(SnpSet,value)<-
:See eSet
pData(SnpSet)
, pData(SnpSet,value)<-
:See eSet
varMetadata(SnpSet)
, varMetadata(SnpSet,value)
See eSet
experimentData(SnpSet)
,experimentData(SnpSet,value)<-
:See eSet
pubMedIds(SnpSet)
, pubMedIds(SnpSet,value)
See eSet
abstract(SnpSet)
:See eSet
annotation(SnpSet)
, annotation(SnpSet,value)<-
See eSet
protocolData(SnpSet)
, protocolData(SnpSet,value)<-
See eSet
combine(SnpSet,SnpSet)
:See eSet
storageMode(eSet)
, storageMode(eSet,character)<-
:See eSet
Standard generic methods:
initialize(SnpSet)
:Object instantiation, used by new
; not to be called directly by the user.
validObject(SnpSet)
:Validity-checking method, ensuring that call
and callProbability
is a member of assayData
. checkValidity(SnpSet)
imposes this validity check, and the validity checks of eSet
.
show(SnpSet)
See eSet
dim(SnpSet)
, ncol
See eSet
SnpSet[(index)
:See eSet
SnpSet$
, SnpSet$<-
See eSet
Martin Morgan, V.J. Carey, after initial design by R. Gentleman
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.