isPm.AffymetrixCdfFile

AffymetrixCdfFile.isPm

isPm,AffymetrixCdfFile-method

The units to be read. 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>, all units are read.

units

Additional arguments passed to <code><a href="/link/readCdfUnits?package=aroma.affymetrix&version=2.2.0&to=affxparser" rd-options="affxparser" data-mini-rdoc="affxparser::readCdfUnits">readCdfUnits</a></code>.

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>, cached results are ignored.

force

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>, results are cached.

cache

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> or <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

Checks which cells (probes) are PMs and not.

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

isPm.AffymetrixCdfFile function

This method caches 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> <code><a href="/link/vector?package=aroma.affymetrix&version=2.2.0&to=base" rd-options="base" data-mini-rdoc="base::vector">vector</a></code> of length N, when N equals the
  number of cells on the array. The size of this vector is approximately
  4*N bytes.  The vector indicates if a cell is a PM or not.

isPm.AffymetrixCdfFile: Checks which cells (probes) are PMs and not

Description

Usage

Arguments

Value

Caching

See Also