setRestructor.AffymetrixCdfFile

AffymetrixCdfFile.setRestructor

setRestructor,AffymetrixCdfFile-method

The units of interest. If <code><a href="/link/NULL?package=aroma.affymetrix&version=2.11.1&to=base" rd-options="base" data-mini-rdoc="base::NULL">NULL</a></code>, all units are considered.

units

Additional arguments passed to
 <code><a href="/link/readCdfCellIndices?package=aroma.affymetrix&version=2.11.1&to=affxparser" rd-options="affxparser" data-mini-rdoc="affxparser::readCdfCellIndices">readCdfCellIndices</a></code>.

Specifies a function through which of all or a subset of the units.

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 disk space that limits the number of arrays that can be analyzed.

Henrik Bengtsson

aroma.affymetrix

Analysis of large Affymetrix microarray data sets

setRestructor.AffymetrixCdfFile function

The reconstructor function have to:
 <ol><li>Accept a<code><a href="/link/list?package=aroma.affymetrix&version=2.11.1&to=base" rd-options="base" data-mini-rdoc="base::list">list</a></code>structure as its first argument.</li><li>Require no other arguments.</li><li>Return a<code><a href="/link/list?package=aroma.affymetrix&version=2.11.1&to=base" rd-options="base" data-mini-rdoc="base::list">list</a></code>structure of identical length as the input one.
 In other words, it must not change the number of units nor
 the order of units.</li></ol> The reconstructor function may:
 <ol><li>Rearrange the groups or change the number of groups, for
 instance by utilizing<code><a href="/link/applyCdfGroups?package=aroma.affymetrix&version=2.11.1&to=affxparser" rd-options="affxparser" data-mini-rdoc="affxparser::applyCdfGroups">applyCdfGroups</a></code>.</li><li>Exclude some cells, for instance by excluding MMs.</li></ol>

setRestructor.AffymetrixCdfFile: Specifies a function through which

Description

Usage

Arguments

Value

Requirements

See Also