attach_ref_spectra

Gathers reference spectra and attaches them to peak_table object. Reference 
spectra are defined either as the spectrum with the highest intensity (
<code>max.int</code>) or as the spectrum with the highest average correlation
to the other spectra in the peak_table (<code>max.cor</code>).

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

attach_ref_spectra function

<dl><dt>peak_table</dt>
<dd>Peak table from <code>get_peaktable</code>.</dd>
<dt>chrom_list</dt>
<dd>A list of chromatograms in matrix form (timepoints x
wavelengths).</dd>
<dt>ref</dt>
<dd>What criterion to use to select reference spectra.
Current options are maximum correlation (<code>max.cor</code>) or maximum signal
intensity (<code>max.int</code>).</dd></dl>

Arguments

Author

Attach reference spectra — attach_ref_spectra

<dl>

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


<dt>chrom_list</dt>
<dd>A list of chromatograms in matrix form (timepoints x
wavelengths).</dd>


<dt>ref</dt>
<dd>What criterion to use to select reference spectra.
Current options are maximum correlation (<code>max.cor</code>) or maximum signal
intensity (<code>max.int</code>).</dd>

</dl>

Data Engineering and BI courses are free this week!

attach_ref_spectra: Attach reference spectra

Description

Usage

Value

Arguments

Author

See Also

Examples