computeAffinities.AffymetrixCdfFile

AffymetrixCdfFile.computeAffinities

computeAffinities,AffymetrixCdfFile-method

A <code><a href="/link/logical?package=aroma.affymetrix&version=2.2.0&to=base" rd-options="base" data-mini-rdoc="base::logical">logical</a></code> argument passed to <code>getProbeSequenceData()</code>.

safe

If <code><a href="/link/FALSE?package=aroma.affymetrix&version=2.2.0&to=base%3Alogical" rd-options="base:logical" data-mini-rdoc="base:logical::FALSE">FALSE</a></code>, cached results is returned, if available.

force

See <code><a href="/link/Verbose?package=aroma.affymetrix&version=2.2.0&to=R.utils" rd-options="R.utils" data-mini-rdoc="R.utils::Verbose">Verbose</a></code>.

verbose

Calculates probe affinities from sequence.

Adapted from <code><a href="/link/compute.affinities?package=aroma.affymetrix&version=2.2.0&to=gcrma" rd-options="gcrma" data-mini-rdoc="gcrma::compute.affinities">compute.affinities</a></code> in the <pkg>gcrma</pkg> package.
Attempts to find the tab-separated probe sequence file associated with
a particular CDF, and matches sequence to probe index in order to assign
an affinity to each probe.

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").

computeAffinities.AffymetrixCdfFile: Calculates probe affinities from sequence

Description

Usage

Arguments

Value