read.AnnotatedDataFrame       package:Biobase       R Documentation

Read 'AnnotatedDataFrame'

Description:

     Create an instance of class AnnotatedDataFrame by reading a file.

Usage:

     read.AnnotatedDataFrame(filename, path,
          sep = "\t", header = TRUE, quote = "", stringsAsFactors = FALSE, 
          row.names = 1L,
          varMetadata.char="#",
          widget = getOption("BioC")$Base$use.widgets,
          sampleNames = character(0), ...) 

Arguments:

filename: file or connection from which to read.

    path: (optional) directory in which to find 'filename'.

row.names: this argument gets passed on to 'read.table' and will be
          used for the row names of the phenoData slot.

varMetadata.char: lines beginning with this character are used for the
          'varMetadata' slot. See examples.

sep, header, quote, stringsAsFactors, ...: further arguments that get
          passed on to 'read.table'.

  widget: logical. Currently this is _not_ implemented, and setting
          this option to 'TRUE' will result in an error. In a precursor
          of this function, 'read.phenoData', this option could be used
          to open an interactive GUI widget for entering the data.

sampleNames: optional argument that could be used in conjunction with
          'widget'; do not use.

Details:

     The function 'read.table' is used to read 'pData'. The argument
     'varMetadata.char' is passed on to that function as its argument
     'comment.char'. Lines beginning with  'varMetadata.char' are
     expected to contain further information on the column headers of
     'pData'. The format is of the form: '# variable: textual
     explanation of the variable, units, measurement method, etc.'
     (assuming that '#' is the value of 'varMetadata.char'). See also
     examples.

Value:

     An instance of class 'AnnotatedDataFrame'

Author(s):

     Martin Morgan <mtmorgan@fhcrc.org> and Wolfgang Huber, based on
     'read.phenoData' by Rafael A. Irizarry.

See Also:

     'AnnotatedDataFrame' for additional methods, 'read.table' for
     details of reading in phenotypic data

Examples:

     exampleFile = system.file("extdata", "pData.txt", package="Biobase")

     adf <- read.AnnotatedDataFrame(exampleFile)
     adf
     head(pData(adf))
     head(readLines(exampleFile))

