updateApdUnits.default

updateApdUnits

Updates an Affymetrix probe data (APD) file by units (probesets) by using the unit and group definitions in the
 corresponding Affymetrix CDF file.

file

DEPRECATED. Do not start building new projects based on this package. (The (in-house) APD file format was initially developed to store Affymetrix probe-level data, e.g. normalized CEL intensities.  Chip types can be added to APD file and similar to methods in the affxparser package, this package provides methods to read APDs organized by units (probesets).  In addition, the probe elements can be arranged optimally such that the elements are guaranteed to be read in order when, for instance, data is read unit by unit.  This speeds up the read substantially.  This package is supporting the Aroma framework and should not be used elsewhere.)

Henrik Bengtsson

aroma.apd

A Probe-Level Data File Format Used by 'aroma.affymetrix'
[deprecated]

updateApdUnits function

<dl> <dt>filename</dt>
<dd>The filename of the APD file.</dd> <dt>units</dt>
<dd>An <code><a href="/link/integer?package=aroma.apd&version=0.7.0" data-mini-rdoc="aroma.apd::integer">integer</a></code> <code><a href="/link/vector?package=aroma.apd&version=0.7.0" data-mini-rdoc="aroma.apd::vector">vector</a></code> of unit indices specifying which
 units to be read. If <code><a href="/link/NULL?package=aroma.apd&version=0.7.0" data-mini-rdoc="aroma.apd::NULL">NULL</a></code>, all units are updated.</dd> <dt>data</dt>
<dd>A <code><a href="/link/numeric?package=aroma.apd&version=0.7.0" data-mini-rdoc="aroma.apd::numeric">numeric</a></code> <code><a href="/link/vector?package=aroma.apd&version=0.7.0" data-mini-rdoc="aroma.apd::vector">vector</a></code> of data elements to be assigned.</dd> <dt>...</dt>
<dd>Additional arguments passed to <code>updateApd</code>(),
 e.g. <code>writeMap</code>.</dd> <dt>cdf</dt>
<dd>A <code><a href="/link/character?package=aroma.apd&version=0.7.0" data-mini-rdoc="aroma.apd::character">character</a></code> filename of a CDF file, or a CDF <code><a href="/link/list?package=aroma.apd&version=0.7.0" data-mini-rdoc="aroma.apd::list">list</a></code>
 structure. If <code><a href="/link/NULL?package=aroma.apd&version=0.7.0" data-mini-rdoc="aroma.apd::NULL">NULL</a></code>, the CDF file is searched for by
 <code>findCdf</code>.</dd> <dt>stratifyBy</dt>
<dd>Argument passed to low-level method
 <code>readCdfCellIndices</code>.</dd> <dt>verbose</dt>
<dd>See <code>Verbose</code>.</dd></dl>

Arguments

Author

Updates an Affymetrix probe data (APD) file by units (probesets) — updateApdUnits

<dl>

 <dt>filename</dt>
<dd>The filename of the APD file.</dd>

 <dt>units</dt>
<dd>An <code><a href='https://rdrr.io/r/base/integer.html'>integer</a></code> <code><a href='https://rdrr.io/r/base/vector.html'>vector</a></code> of unit indices specifying which
 units to be read. If <code><a href='https://rdrr.io/r/base/NULL.html'>NULL</a></code>, all units are updated.</dd>

 <dt>data</dt>
<dd>A <code><a href='https://rdrr.io/r/base/numeric.html'>numeric</a></code> <code><a href='https://rdrr.io/r/base/vector.html'>vector</a></code> of data elements to be assigned.</dd>

 <dt>...</dt>
<dd>Additional arguments passed to <code>updateApd</code>(),
 e.g. <code>writeMap</code>.</dd>

 <dt>cdf</dt>
<dd>A <code><a href='https://rdrr.io/r/base/character.html'>character</a></code> filename of a CDF file, or a CDF <code><a href='https://rdrr.io/r/base/list.html'>list</a></code>
 structure. If <code><a href='https://rdrr.io/r/base/NULL.html'>NULL</a></code>, the CDF file is searched for by
 <code>findCdf</code>.</dd>

 <dt>stratifyBy</dt>
<dd>Argument passed to low-level method
 <code>readCdfCellIndices</code>.</dd>

 <dt>verbose</dt>
<dd>See <code>Verbose</code>.</dd>

</dl>

updateApdUnits: Updates an Affymetrix probe data (APD) file by units (probesets)

Description

Usage

Value

Arguments

Author

See Also