| 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. annotationexprSet instance.description:characterOrMIAME has been
defined just for this.notes:signature(object = "exprExternal"): An accessor
function for the exprs.ext slot. signature(exprExternal, missing, function): An
iteratorover genes. Returns the result of applying function
to the matrix of expressions on margin 1 (see apply)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)))