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]