dataset-class {magpie} | R Documentation |
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.
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.
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.
dataId
:character
. Identifier of the data setdataPath
:character
. Path where the files of the data set are storedgeneExprFile
:character
. Name of the gene expression fileclassesFile
:character
. Name of the output classes fileeset
:ExpressionSetOrNull
. NULL
if the data set has not been loaded yet or Object of class ExpressionSet
containing the microarray datagetClassesFile(dataset)
, getClassesFile(dataset)<-
getDataId(dataset)
, getDataId(dataset)<-
getDataPath(dataset)
, getDataPath(dataset)<-
getEset(dataset)
getGeneExprFile(dataset)
, getGeneExprFile(dataset)<-
Camille Maumet
## 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)