exprExternal-class {exprExternal} | R Documentation |
This is a class representing Microarray Data. Unlike
its parent class exprSet
, this class uses reference to an external
matrix object for storing the gene expression data.
Objects can be created by either using
as(x, "exprExternal")
where x
is an object of class exprSet
or by a call of the
form
new('exprExternal',
exprs.ext = ...., # Object of class indirectExternalMatrix
se.exprs.ext = ...., # Object of class indirectExternalMatrix
phenoData = ...., # Object of class phenoData
annotation = ...., # Object of class character
description = ...., # Object of class MIAME
notes = ...., # Object of class character
)
exprs.ext
:externalVector
of two dimensions with columns
representing patients or cases and rows representing genes. se.exprs.ext
:externalVector
of the same dimensions as
exprs
which contains
standard error estimates for the estimated expression levels or
reference to an object of class externalVector
of length
zero. phenoData
:phenoData
containing the patient (or case) level data. The columns of the
pData slot of this entity represent
variables and the rows represent patients or cases. annotation
exprSet
instance.description
:characterOrMIAME
has been
defined just for this.notes
:signature(object = "exprExternal")
: An accessor
function for the exprs.ext slot. signature(object = "exprExternal")
: An accessor
function for the se.exprs.ext slot. signature(x = "exprExternal")
:
Writes the expression levels to csv
file. This file will open nicely in excel. It takes the same
arguments as write.table
. If
called with no arguments it is equivalent to
write.table(force(exprs(exprSet))[,],file="tmp.csv", sep = ",", col.names = NA)
.signature(x = "exprExternal")
:
Writes the expression levels to
file. It takes the same arguments as write.table
. If
called with no arguments it is equivalent to
write.table(force(exprs(exprSet))[,],file="tmp.txt",quote=FALSE,sep="t").signature(from = "exprSet", to = "exprExternal")
:
Convert an object of class exprSet
to an equivalent object of
class exprExternal
. This is almost never called
directly. Instead, useas(exprSet, "exprExternal")
## Run the examples from exprSet manual page library('externalVector') library('Biobase') data(geneData) data(geneCov) covdesc<- list("Covariate 1", "Covariate 2", "Covariate 3") names(covdesc) <- names(geneCov) pdata <- new("phenoData", pData=geneCov, varLabels=covdesc) pdata[1,] pdata[,2] eset <- as(new("exprSet", exprs=geneData, phenoData=pdata), "exprExternal") eset eset[,1:10] eset[,1] eset[1,] eset[1,1] eset[1:100,] eset[1:44,c(2,4,6)] Means <- iter(eset, f=mean) sp1 <- split(eset, c(1,2)) sp2 <- split(eset, c(rep(1,6), rep(2,7)))