readExpressionSet {Biobase}R Documentation

Read 'ExpressionSet'

Description

Create an instance of class ExpressionSet by reading data from files.

Unfortunately, 'widget' functionality is not yet implemented for read.ExpressionSet.

Usage

readExpressionSet(exprsFile,
                   phenoDataFile=character(0),
                   experimentDataFile=character(0),
                   notesFile=character(0),
                   annotation=character(0),
                   ## arguments to read.* methods 
                   exprsArgs=list(...),
                   phenoDataArgs=list(...),
                   experimentDataArgs=list(...),
                   notesArgs=list(...),
                   ## widget
                   widget = getOption("BioC")$Base$use.widgets,
                   ...)

Arguments

exprsFile (character) File name from which to read expression values. File should contain a matrix with rows as features and columns as samples. Tab-delimited files can be read with the additional argument sep="\t".
phenoDataFile (character) File name from which to read phenotypic data. See read.AnnotatedDataFrame for details.
experimentDataFile (character) File name from which to read experiment data. See read.MIAME for details.
notesFile (character) File name from which to read notes; readLines is used to input the file.
annotation (character) A single character string indicating the annotation associated with this ExpressionSet.
exprsArgs A list of arguments to be used (with read.table) when reading in the expression matrix.
phenoDataArgs A list of arguments to be used (with read.AnnotatedDataFrame) when reading phenoData.
experimentDataArgs A list of arguments to be used (with read.MIAME) when reading experiment data.
notesArgs A list of arguments to be used (with readLines) when reading notes.
widget A boolean value indicating whether widgets can be used. Widgets are NOT yet implemented for read.AnnotatedDataFrame.
... Arugments passed by default to all methods used to read data.

Details

Expression values are read using the read.table function. Phenotypic data are read using the read.AnnotatedDataFrame function. Experiment data are read using the read.MIAME function. Notes are read using the readLines function. The return value must be a valid ExpressionSet.

Value

An instance of ExpressionSet-class.

Author(s)

Martin Morgan <mtmorgan@fhcrc.org>

See Also

ExpressionSet for additional methods.

Examples


## Create a temporary file for expression data

exprsFile <- tempfile()
data(geneData)
write.table(geneData[,1:6], exprsFile, quote = FALSE, sep = "\t",
            row.names = TRUE, col.names = TRUE)

## Create a temporary file with a structure like that from 'Save
## as...' text file from a popular spreadsheet (see
## read.AnnotatedDataFrame)

phenoDataFile <- tempfile()
df <- data.frame(Id=paste("Sample", 1:6),
                 x=1:6,
                 y=rep(c("Low", "High"), 3),
                 z=I(letters[1:6]))
write.table(df, phenoDataFile, quote=FALSE, sep="\t", row.names=FALSE)

## Read ExpressionSet with appropriate parameters

obj <- readExpressionSet(exprsFile, phenoDataFile, header=TRUE, sep="\t")
obj

unlink(c("exprsFile", "phenoDataFile"))


[Package Biobase version 1.14.1 Index]