exprExternal-class {exprExternal}R Documentation

Class exprExternal, a subclass of exprSet, and methods for manipulating objects of class exprExternal

Description

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.

Creating Objects

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
)

Slots

exprs.ext:
Object of class "indirectExternalMatrix". The observed expression levels. This contains refernce to an object of class externalVector of two dimensions with columns representing patients or cases and rows representing genes.
se.exprs.ext:
Object of class "indirectExternalMatrix". This either contains reference to an object of class 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:
Object of class "phenoData" This is an instance of class 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
A character string identifying the annotation that may be used for the exprSet instance.
description:
Object of class "MIAME". For compatibility with previous version of this class description can also be a "character". The clase characterOrMIAME has been defined just for this.
notes:
Object of class "character" Vector of explanatory text

Methods

exprs
signature(object = "exprExternal"): An accessor function for the exprs.ext slot.
se.exprs
signature(object = "exprExternal"): An accessor function for the se.exprs.ext slot.
exprs2excel
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).
write.exprs
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").
coerce
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, use
as(exprSet, "exprExternal")

See Also

exprSet-class

Examples

  ## 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)))

[Package exprExternal version 1.0.0 Index]