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 readExpressionSet.

### Usage

    readExpressionSet(exprsFile,
          phenoDataFile,
          experimentDataFile,
          notesFile,
          path,
          annotation,
          ## arguments to read.* methods
          exprsArgs=list(sep=sep, header=header, row.names=row.names, quote=quote, ...),
          phenoDataArgs=list(sep=sep, header=header, row.names=row.names, quote=quote, stringsAsFactors=stringsAsFactors, ...),
          experimentDataArgs=list(sep=sep, header=header, row.names=row.names, quote=quote, stringsAsFactors=stringsAsFactors, ...),
          sep = "\t", header = TRUE, quote = "", stringsAsFactors = FALSE, row.names = 1L,
          ## widget
          widget = getOption("BioC")$Base$use.widgets,
          ...)

### Arguments

`exprsFile` | (character) File or connection from which to read expression values. The file should contain a matrix with rows as features and columns as samples. `read.table` is called with this as its `file` argument and further arguments given by `exprsArgs`.
`phenoDataFile` | (character) File or connection from which to read phenotypic data. `read.AnnotatedDataFrame` is called with this as its `file` argument and further arguments given by `phenoDataArgs`.
`experimentDataFile` | (character) File or connection from which to read experiment data. `read.MIAME` is called with this as its `file` argument and further arguments given by `experimentDataArgs`.
`notesFile` | (character) File or connection from which to read notes; `readLines` is used to input the file.
`path` | (optional) directory in which to find all the above files.
`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 the phenotypic data.
`experimentDataArgs` | A list of arguments to be used (with `read.MIAME`) when reading the experiment data.
`sep, header, quote, stringsAsFactors, row.names` | arguments used by the `read.table`-like functions.
`widget` | A boolean value indicating whether widgets can be used. Widgets are NOT yet implemented for `read.AnnotatedDataFrame`.
`...` | Further arguments that can be passed on to the `read.table`-like functions.

### 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 the `ExpressionSet` class.

### Author(s)

Martin Morgan <mtmorgan@fhcrc.org>

### See Also

`ExpressionSet` for additional methods.

### Examples

    exprsFile = system.file("extdata", "exprsData.txt", package="Biobase")
    phenoFile = system.file("extdata", "pData.txt", package="Biobase")

    ## Read ExpressionSet with appropriate parameters
    obj = readExpressionSet(exprsFile, phenoFile, sep = "\t", header=TRUE)
    obj

[Package Biobase version 2.0.1 Index]