readExpressionSet          package:Biobase          R Documentation

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>

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

