dataset-class {magpie}R Documentation

dataset: A simple class to store a microarray dataset and its related files

Description

This class is designed to store the location of the files corresponding to a microarray data set and convert it to an ExpressionSet object on demand.

Details

The microarray data set must consists of two files: a gene expression file and an output classes files. The gene expression file must be a table of gene expression values. Usually, each column corresponds to a sample and each row to a gene but the other way around is valid too. The first line can be used as a header corresponding to the names of the sample (or genes depending on the order) and the first column to the names of the genes (or samples). The classes output file contains one line (or column) of values reflecting the class belonging of each sample.

Creating objects

new("dataset", dataId, dataPath = "./")

Creates a dataset with identifier dataId. The two files containing the gene expression profiles and the output classes must be available in the folder pointed by dataPath. The slots geneExprFile and classesFile are automatically generated and corresponds respectively to the concatenation of the dataId with "_geneExpr.txt" and "_classes.txt". If the user wants to specify custom names for the files he can use one of the following command lines to create his dataset.

new("dataset", dataId, dataPath = "./", geneExprFile)

Creates a dataset with identifier dataId. The two files containing the gene expression profiles and the output classes must be available in the folder pointed by dataPath. classesFile is automatically generated and corresponds to the concatenation of the dataId with "_classes.txt". geneExprFile is the name of the file containing the gene expression profiles.

new("dataset", dataId, dataPath = "./", classesFile)

Create a dataset with identifier dataId. The two files containing the gene expression profiles and the output classes must be available in the folder pointed by dataPath. geneExprFile is automatically generated as the concatenation of the dataId with "_geneExpr.txt". classesFile is the name of the file containing the output classes for each sample.

Slots

dataId:
character. Identifier of the data set
dataPath:
character. Path where the files of the data set are stored
geneExprFile:
character. Name of the gene expression file
classesFile:
character. Name of the output classes file
eset:
ExpressionSetOrNull. NULL if the data set has not been loaded yet or Object of class ExpressionSet containing the microarray data

Methods

getClassesFile(dataset), getClassesFile(dataset)<-
Retrieve and Modify the name of the output classes file (slot classesFile)
getDataId(dataset), getDataId(dataset)<-
Retrieve and Modify the identifier of the data set (slot dataId)
getDataPath(dataset), getDataPath(dataset)<-
Retrieve and Modify the identifier of path where the files of the data set are stored (slot dataPath)
getEset(dataset)
If the data set has already been loaded, retrieve the expression set containing the data set, if not return NULL (slot eset)
getGeneExprFile(dataset), getGeneExprFile(dataset)<-
Retrieve and Modify the name of the gene expression file (slot geneExprFile)

Author(s)

Camille Maumet

See Also

experiment

Examples

## Not run: 
    dataPath <- "C:/Documents and Settings/c.maumet/My Documents/Programmation/Sources/SVN/R package/data"
    vantVeerData <- new("dataset", dataId="khan", dataPath=dataPath )

    getDataId(vantVeerData)
    getDataId(vantVeerData) <- "vantVeer_70"

    getDataPath(vantVeerData)
    getEset(vantVeerData)

    getGeneExprFile(vantVeerData)
    otherValidFile <- "vantVeer_70_geneExpr_copie.txt"
    getGeneExprFile(vantVeerData) <- otherValidFile
    getGeneExprFile(vantVeerData)
    getClassesFile(vantVeerData)
    otherValidFile <- "vantVeer_70_classes_copie.txt"
    getClassesFile(vantVeerData) <- otherValidFile
    getClassesFile(vantVeerData)

    loadData(vantVeerData)

    vantVeerData <- new("dataset", dataId="khan", dataPath=dataPath )
    miame <- new("MIAME")
    annotation <- "hghjgjg"
    loadData(vantVeerData, miame, annotation)
## End(Not run)


[Package magpie version 0.2.0 Index]