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    <p>You can see what slots are available in your <code>xcmsRaw</code> instance with </p> <pre><code>&gt; slotNames(xraw) [1] "env" "tic" "scantime" [4] "scanindex" "polarity" "acquisitionNum" [7] "profmethod" "profparam" "mzrange" [10] "gradient" "msnScanindex" "msnAcquisitionNum" [13] "msnPrecursorScan" "msnLevel" "msnRt" [16] "msnPrecursorMz" "msnPrecursorIntensity" "msnPrecursorCharge" [19] "msnCollisionEnergy" "filepath" </code></pre> <p>What you want is <code>xraw@msnRt</code> - it is a <code>vector</code> of <code>numeric</code>.</p> <p>The <code>env</code> slot is a environment that stores 3 variables:</p> <pre><code>&gt; ls(xraw@env) [1] "intensity" "mz" "profile" </code></pre> <p>More details on the class itself at <code>class?xcmsRaw</code>.</p> <p><strong>EDIT:</strong> The <code>msnRt</code> slot is populated only if you specify <code>includeMSn = TRUE</code> and your input file must be in <code>mzXML</code> or <code>mzML</code>, not in <code>cdf</code>; if you use the <code>faahKO</code> example from <code>?xcmasRaw</code>, you will see that </p> <pre><code>xr &lt;- xcmsRaw(cdffiles[1], includeMSn = TRUE) Warning message: In xcmsRaw(cdffiles[1], includeMSn = TRUE) : Reading of MSn spectra for NetCDF not supported </code></pre> <p>Also, <code>xr@msnRt</code> will only store the retention times for MSn scans, with <code>n &gt; 1</code>. See the <code>xset@rt</code> where <code>xset</code> is an <code>xcmsSet</code> instance for the raw/corrected MS1 retention times as provided by <code>xcms</code>.</p> <p><strong>EDIT2:</strong> Alternatively, have a go with the <a href="http://www.bioconductor.org/packages/release/bioc/html/mzR.html" rel="nofollow"><code>mzR</code></a> package</p> <pre><code>&gt; library(mzR) &gt; cdffiles[1] [2] "/home/lgatto/R/x86_64-unknown-linux-gnu-library/2.16/faahKO/cdf/KO/ko15.CDF" &gt; xx &lt;- openMSfile(cdffiles[1]) &gt; xx Mass Spectrometry file handle. Filename: /home/lgatto/R/x86_64-unknown-linux-gnu-library/2.16/faahKO/cdf/KO/ko15.CDF Number of scans: 1278 &gt; hd &lt;- header(xx) &gt; names(hd) [1] "seqNum" "acquisitionNum" [3] "msLevel" "peaksCount" [5] "totIonCurrent" "retentionTime" [7] "basePeakMZ" "basePeakIntensity" [9] "collisionEnergy" "ionisationEnergy" [11] "highMZ" "precursorScanNum" [13] "precursorMZ" "precursorCharge" [15] "precursorIntensity" "mergedScan" [17] "mergedResultScanNum" "mergedResultStartScanNum" [19] "mergedResultEndScanNum" &gt; class(hd) [1] "data.frame" &gt; dim(hd) [1] 1278 19 </code></pre> <p>but you will be outside of the default <code>xcms</code> pipeline if you take this route (although Steffen Neumann, from <code>xcms</code>, does know <code>mzR</code> very well, oubviously).</p> <p>Finally, you are better of to use the Bioconductor <a href="http://bioconductor.org/help/mailing-list/" rel="nofollow">mailing list</a> of the <a href="http://www.metabolomics-forum.com/viewforum.php?f=10" rel="nofollow"><code>xcms</code> online forum</a> if you want to maximise your chances to get feedback from the <code>xcms</code> developers. </p> <p>Hope this helps.</p>
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