Biobase: readExpressionSet – R documentation

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readExpressionSet

Read 'ExpressionSet'

Description

Create an instance of class ExpressionSet by reading data from files. ‘widget’ functionality is not 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. Only the exprsFile argument is required.

Value

An instance of the ExpressionSet class.

Author(s)

Martin Morgan <mtmorgan@fhcrc.org>

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

Biobase

Biobase: Base functions for Bioconductor

v2.50.0

Artistic-2.0

Authors

R. Gentleman, V. Carey, M. Morgan, S. Falcon

Initial release