combine_peaks

Utility function to combine duplicate peaks in peak table, i.e. peaks that
were integrated at more than one wavelength or component. Specify tolerance
(<code>tol</code>) for retention time matching and minimum spectral correlation
(<code>min.cor</code>) for a match.

Tools for high-throughput analysis of HPLC-DAD/UV
chromatograms (or similar data). Includes functions for preprocessing, alignment,
peak-finding and fitting, peak-table construction, data-visualization, etc.
Preprocessing and peak-table construction follow the rough formula laid out
in alsace (Wehrens, R., Bloemberg, T.G., and Eilers P.H.C., 2015.
<doi:10.1093/bioinformatics/btv299>. Alignment of chromatograms is available
using parametric time warping (ptw) (Wehrens, R., Bloemberg, T.G., and Eilers
P.H.C. 2015. <doi:10.1093/bioinformatics/btv299>) or variable penalty dynamic
time warping (VPdtw) (Clifford, D., & Stone, G. 2012. <doi:10.18637/jss.v047.i08>).
Peak-finding uses the algorithm by Tom O'Haver
<http://terpconnect.umd.edu/~toh/spectrum/PeakFindingandMeasurement.htm>.
Peaks are then fitted to a gaussian or exponential-gaussian hybrid peak shape
using non-linear least squares (Lan, K. & Jorgenson, J. W. 2001.
<doi:10.1016/S0021-9673(01)00594-5>). See the vignette for more details and
suggested workflow.

Ethan Bass

chromatographR

Chromatographic Data Analysis Toolset

combine_peaks function

<dl><dt>peak_table</dt>
<dd>Peak table from <code>get_peaktable</code>.</dd>
<dt>tol</dt>
<dd>Tolerance for matching retention times (maximum retention time
difference).</dd>
<dt>min.cor</dt>
<dd>Minimum spectral correlation to confirm a match.</dd>
<dt>choose</dt>
<dd>If "max" will retain peak with highest intensity. Otherwise,
the first column in the data.frame will be retained.</dd></dl>

Arguments

Author

Combine peaks in peak table — combine_peaks

<dl>

<dt>peak_table</dt>
<dd>Peak table from <code>get_peaktable</code>.</dd>


<dt>tol</dt>
<dd>Tolerance for matching retention times (maximum retention time
difference).</dd>


<dt>min.cor</dt>
<dd>Minimum spectral correlation to confirm a match.</dd>


<dt>choose</dt>
<dd>If "max" will retain peak with highest intensity. Otherwise,
the first column in the data.frame will be retained.</dd>

</dl>

combine_peaks: Combine peaks in peak table

Description

Usage

Value

Arguments

Author

See Also

Examples