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XCMS Get Alignment EICs (version 0.0.4)
E.g. output data file resulting from METAMS run
Start of Retention Time region to plot
End of Retention Time region to plot
Can also read this as: Minimum number of features in alignment. E.g. if set to 10, it means the alignment should consist of at least 10 peaks from 10 different samples aligned together.
Comma or line-separated list of sample names. Optional field where you can specify the subset of samples to use for the EIC plots. NB: if your dataset has many samples, specifying a subset here can significantly speed up the processing time.

This tool finds the alignments in the specified RT window and extracts alignment EICs from feature alignment data using XCMS's getEIC method. It produces a HTML report showing the EIC plots and the mass list of each alignment. The figure below shows an example of such an EIC plot, showing also the difference between two classes, with extra alignment information beneath it.

/repository/static/images/02534e21e01840b4/diffreport.png

Alignment id: 1709. m/z list of peaks in alignment: 614.002922098482,613.998019830021,614.000382307519,613.998229980469,613.998229980469