cdfToApdMap.default

cdfToApdMap

Generates an APD read map file from an 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]

cdfToApdMap function

<dl> <dt>filename</dt>
<dd>The pathname of the CDF file.</dd> <dt>mapType</dt>
<dd>A <code><a href="/link/character?package=aroma.apd&version=0.7.0" data-mini-rdoc="aroma.apd::character">character</a></code> string naming the type of the map.
 If <code><a href="/link/NULL?package=aroma.apd&version=0.7.0" data-mini-rdoc="aroma.apd::NULL">NULL</a></code>, the chip type will be used.</dd> <dt>mapFile</dt>
<dd>The filename of the resulting APD map file. If <code><a href="/link/NULL?package=aroma.apd&version=0.7.0" data-mini-rdoc="aroma.apd::NULL">NULL</a></code>,
 the map type with filename extension <code>apm</code> will be used.</dd> <dt>mapPath</dt>
<dd>An optional path where to the map file will be stored.</dd> <dt>...</dt>
<dd>Additional arguments passed to
 <code>readCdfUnitsWriteMap</code>, e.g. <code>units</code>.</dd> <dt>verbose</dt>
<dd>A <code>Verbose</code> object.</dd></dl>

Arguments

Author

Generates an APD read map file from an Affymetrix CDF file — cdfToApdMap

<dl>

 <dt>filename</dt>
<dd>The pathname of the CDF file.</dd>

 <dt>mapType</dt>
<dd>A <code><a href='https://rdrr.io/r/base/character.html'>character</a></code> string naming the type of the map.
 If <code><a href='https://rdrr.io/r/base/NULL.html'>NULL</a></code>, the chip type will be used.</dd>

 <dt>mapFile</dt>
<dd>The filename of the resulting APD map file. If <code><a href='https://rdrr.io/r/base/NULL.html'>NULL</a></code>,
 the map type with filename extension <code>apm</code> will be used.</dd>

 <dt>mapPath</dt>
<dd>An optional path where to the map file will be stored.</dd>

 <dt>...</dt>
<dd>Additional arguments passed to
 <code>readCdfUnitsWriteMap</code>, e.g. <code>units</code>.</dd>

 <dt>verbose</dt>
<dd>A <code>Verbose</code> object.</dd>

</dl>

cdfToApdMap: Generates an APD read map file from an Affymetrix CDF file

Description

Usage

Value

Arguments

Author

See Also