byPath.AffymetrixFileSet

AffymetrixFileSet.byPath

byPath,AffymetrixFileSet-method

The path where to search for Affymetrix files.

path

The filename pattern for match files.
    If <code><a href="/link/NULL?package=aroma.affymetrix&version=2.2.0&to=base" rd-options="base" data-mini-rdoc="base::NULL">NULL</a></code>, filename extensions corresponding to known subclasses
    of the abstract <code><a href="/link/AffymetrixFile?package=aroma.affymetrix&version=2.2.0" rd-options="" data-mini-rdoc="aroma.affymetrix::AffymetrixFile">AffymetrixFile</a></code> class a

pattern

If <code><a href="/link/TRUE?package=aroma.affymetrix&version=2.2.0&to=base%3Alogical" rd-options="base:logical" data-mini-rdoc="base:logical::TRUE">TRUE</a></code>, subdirectories are search recursively,
    otherwise not.

recursive

Optional arguments passed to the constructor of the
    static (calling) class.

Defines an AffymetrixFileSet object by searching for Affymetrix files.

methods

internal

This package implements classes for files and sets of
        files for various Affymetrix file formats, e.g.
        AffymetrixCdfFile, AffymetrixCelFile, and AffymetrixCelSet.
        These are designed to be memory efficient but still being fast.
        The idea is to keep all data on file and only read data into
        memory when needed.  Clever caching mechanisms are used to
        minimize the overhead of data IO.  All of the above is hidden
        in the package API and for the developer (and the end user),
        the data is queried as if it lives in memory.  With this design
        it is only the diskspace that limits the number of arrays that
        can be analyzed.  To install, do:
        source("http://www.aroma-project.org/hbLite.R");
        hbInstall("aroma.affymetrix").

Henrik Bengtsson

aroma.affymetrix

Analysis of large Affymetrix microarray data sets

byPath.AffymetrixFileSet function

byPath.AffymetrixFileSet(static, ..., fileClass="AffymetrixFile")

synopsis

Note that files with names starting with a period <code>.</code> are not
  searched for.  The reason for this is that such files are reserved for
  internal use of this package.  For instance, the package store average
  signals across CEL files in a file named as <code>.average<something>.CEL</something></code>
  in the same directory as the CEL files, and when such a directory is
  scanned we do not want such files to be interpreted as data.

byPath.AffymetrixFileSet: Defines an AffymetrixFileSet object by searching for Affymetrix files

Description

Usage

Arguments

Value

synopsis

Reserved filenames

See Also