exprSet-class {Biobase}R Documentation

Class exprSet, a class for microarray data, and methods for processing them

Description

This is class representation for Microarray Data

Creating Objects

new('exprSet',
exprs = ...., # Object of class matrix
se.exprs = ...., # Object of class matrix
phenoData = ...., # Object of class phenoData
annotation = ...., # Object of class character
description = ...., # Object of class MIAME
notes = ...., # Object of class character
)

Slots

exprs:
Object of class "matrix" The observed expression levels. This is a matrix with columns representing patients or cases and rows representing genes.
se.exprs:
Object of class "matrix" This is a matrix of the same dimensions as exprs which contains standard error estimates for the estimated expression levels.
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

[
(exprSet): A subset operator. Ensures that both exprs and phenoData are subset properly.
[[
(exprSet): Extract the named variable from the phenoData component.
exprs
(exprSet): An accessor function for exprs.
se.exprs
(exprSet): An accessor function for se.exprs.
description
(exprSet): Obtain the description (MIAME class) of exprSet.
description<-
(exprSet): Set the description (MIAME class) of exprSet.
notes
(exprSet): Obtain the notes of exprSet.
notes<-
(exprSet): Set the notes of exprSet.
geneNames
(exprSet): Obtain the gene names (row names) of exprs.
geneNames<-
(exprSet): Set the gene names (row names) of exprs.
iter
(exprSet, missing, function): an iterator over genes. Returns the result of applying function to the matrix of expressions on margin 1 (see apply)
iter
(exprSet, missing, list): a multi-iterator over genes. Concatenates result of applying each function in the list list in a matrix (assumes result of each function evaluation is a scalar).
iter
(exprSet, covlab=character, function): a iterator over genes: function is assumed to have arguments x and y; the pData element named by covlab will be bound to x, the gene expression values will be iteratively bound to y
phenoData
(exprSet): An accessor function returns the phenoData instance from the exprSet.
pData
(exprSet): An accessor function for the pData slot of the phenoData contained in the instance.
pData<-
(exprSet): A replacement method for the pData slot of the phenoData contained in the instance.
sampleNames
(exprSet): An accessor function for sample labels. These are the column labels of exprs and the row labels from pData. The function takes preferably the column labels of exprs (if any).
sampleNames<-
(exprSet): A replacement method that sets the sample names to new values. The values must be character and the length of the vector must be equal to the number of samples.
show
(exprSet): renders information about the exprSet in a concise way on stdout.
split
(exprSet, vector): splits the exprSet. The returned value is a list, each component of which is an exprSet. If the length of vector is a divisor of the number of rows in the expression array then the expression array is split. Subsequently, if the length of vector is a divisor of the number of rows of the phenoData data frame then the split is made on this.
annotation
(exprSet): An accessor function for the annotation information.
write.exprs
(exprSet,...): 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(exprs(exprSet),file="tmp.txt",quote=FALSE,sep="t").
exprs2excel
(exprSet,...): 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(exprs(exprSet),file="tmp.csv", sep = ",", col.names = NA).
$
An old-style method. It is pData(eset)[[as.character(val)]] which does not quite have the right semantics but it is close. This operator extracts the named component of the pData slot in phenoData.
update2MIAME
(exprSet,...): Converts exprSets from previous versions, that have a character in description to an object that has an instance of the class MIAME in the description slot. The old description is stored in the title slot. If the object already has a MIAME description the same object is returned.

See Also

MIAME-class

Examples

  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 <- new("exprSet", exprs=geneData, phenoData=pdata)
  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)

  chkdich <- function(x) if(length(unique(x))!=2) stop("x not dichotomous")
  mytt <- function(x,y) {
     chkdich(x)
     d <- split(y,x)
     t.test(d[[1]],d[[2]])$p.val
  }
  
  Tpvals <- iter(eset, "cov1", mytt )

  sp1 <- split(eset, c(1,2))
  sp2 <- split(eset, c(rep(1,6), rep(2,7)))

  sampleNames(eset)
  sampleNames(eset) <- letters

[Package Biobase version 1.4.15 Index]