Package org.rosuda.JRI

Examples of org.rosuda.JRI.Rengine.eval()

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      rEngine.assign("mass", masses);
      rEngine.assign("intensity", intensities);

      // Construct xcmsRaw object
      rEngine.eval("xRaw <- new(\"xcmsRaw\")", false);
      rEngine.eval("xRaw@tic <- intensity", false);
      rEngine.eval("xRaw@scantime <- scantime * " + SECONDS_PER_MINUTE,
          false);
      rEngine.eval("xRaw@scanindex <- scanindex", false);
      rEngine.eval("xRaw@env$mz <- mass", false);
      rEngine.eval("xRaw@env$intensity <- intensity", false);
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      rEngine.assign("intensity", intensities);

      // Construct xcmsRaw object
      rEngine.eval("xRaw <- new(\"xcmsRaw\")", false);
      rEngine.eval("xRaw@tic <- intensity", false);
      rEngine.eval("xRaw@scantime <- scantime * " + SECONDS_PER_MINUTE,
          false);
      rEngine.eval("xRaw@scanindex <- scanindex", false);
      rEngine.eval("xRaw@env$mz <- mass", false);
      rEngine.eval("xRaw@env$intensity <- intensity", false);

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      // Construct xcmsRaw object
      rEngine.eval("xRaw <- new(\"xcmsRaw\")", false);
      rEngine.eval("xRaw@tic <- intensity", false);
      rEngine.eval("xRaw@scantime <- scantime * " + SECONDS_PER_MINUTE,
          false);
      rEngine.eval("xRaw@scanindex <- scanindex", false);
      rEngine.eval("xRaw@env$mz <- mass", false);
      rEngine.eval("xRaw@env$intensity <- intensity", false);

      // Create the xcmsSet object.
      rEngine.eval("xs <- new('xcmsSet')", false);
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      rEngine.eval("xRaw <- new(\"xcmsRaw\")", false);
      rEngine.eval("xRaw@tic <- intensity", false);
      rEngine.eval("xRaw@scantime <- scantime * " + SECONDS_PER_MINUTE,
          false);
      rEngine.eval("xRaw@scanindex <- scanindex", false);
      rEngine.eval("xRaw@env$mz <- mass", false);
      rEngine.eval("xRaw@env$intensity <- intensity", false);

      // Create the xcmsSet object.
      rEngine.eval("xs <- new('xcmsSet')", false);

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      rEngine.eval("xRaw@tic <- intensity", false);
      rEngine.eval("xRaw@scantime <- scantime * " + SECONDS_PER_MINUTE,
          false);
      rEngine.eval("xRaw@scanindex <- scanindex", false);
      rEngine.eval("xRaw@env$mz <- mass", false);
      rEngine.eval("xRaw@env$intensity <- intensity", false);

      // Create the xcmsSet object.
      rEngine.eval("xs <- new('xcmsSet')", false);

      // Set peaks.
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      rEngine.eval("xRaw@scanindex <- scanindex", false);
      rEngine.eval("xRaw@env$mz <- mass", false);
      rEngine.eval("xRaw@env$intensity <- intensity", false);

      // Create the xcmsSet object.
      rEngine.eval("xs <- new('xcmsSet')", false);

      // Set peaks.
      rEngine.eval("xs@peaks <- peaks", false);

      // Set file (dummy) file path.
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      // Create the xcmsSet object.
      rEngine.eval("xs <- new('xcmsSet')", false);

      // Set peaks.
      rEngine.eval("xs@peaks <- peaks", false);

      // Set file (dummy) file path.
      rEngine.eval("xs@filepaths  <- ''", false);

      // Set sample name.
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      // Set peaks.
      rEngine.eval("xs@peaks <- peaks", false);

      // Set file (dummy) file path.
      rEngine.eval("xs@filepaths  <- ''", false);

      // Set sample name.
      rEngine.assign("sampleName", peakList.getName());
      rEngine.eval("sampnames(xs) <- sampleName", false);
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      // Set file (dummy) file path.
      rEngine.eval("xs@filepaths  <- ''", false);

      // Set sample name.
      rEngine.assign("sampleName", peakList.getName());
      rEngine.eval("sampnames(xs) <- sampleName", false);

      // Create an empty xsAnnotate.
      rEngine.eval("an <- xsAnnotate(xs, sample=1)", false);

      // Group by RT.
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      // Set sample name.
      rEngine.assign("sampleName", peakList.getName());
      rEngine.eval("sampnames(xs) <- sampleName", false);

      // Create an empty xsAnnotate.
      rEngine.eval("an <- xsAnnotate(xs, sample=1)", false);

      // Group by RT.
      rEngine.eval("an <- groupFWHM(an, sigma=" + fwhmSigma
          + ", perfwhm=" + fwhmPercentage + ')', false);
      progress += progressInc;
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