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Scanning Parameters
Scanning Parameters control the initial identification and coarse filtering of peaks. This is the most time intensive step, so these settings should not be changed if it can be avoided.
| Parameter | Description |
|---|---|
| Maxima Window | Final filter to remove close peaks. For each peak identified, take only largest peaks that fall within the window size (in data points) of each other |
There are currently two different algorithms available for use to determine peaks, Relative Maximum and Continuous Wavelet Transform. Relative Maximum is a fast simple algorithm that finds local maxima by sliding a window across the data and determining the maximum point within that window, thus identifying a peak. The data is first smoothed with a Savitzky-Golay filter and baseline corrected using a white-tophat transform before the Relative Maximum algorithm is applied. Continuous Wavelet Transform is a more complicated algorithm that works by convolving the signal with a series of wavelets from a given set of widths, and then determines peaks that appear at enough length scales and have sufficiently high SNR. In general, Relative Maximum is faster and typically works well enough, although a properly tuned CWT can perform very well in noisy data. More information can be found here http://bioinformatics.oxfordjournals.org/content/22/17/2059.long
| Parameter | Description |
|---|---|
| Relative Maximum Window | Number of points on each side of prospective peak to identify relative maximum |
| Smoothing Window | Window size passed to the Savitzky-Golay filter |
| Smoothing Order | Order of the polynomial used in the Savitzky-Golay filter to smooth the data |
| Tophat Factor | Size Factor to apply the white-tophat filter. Tophat filter footprint size is (Tophat Factor)*(length(signal)) |
| Parameter | Description |
|---|---|
| CWT Min Width | Minimum expected peak width |
| CWT Max Width | Maximum expected peak width |
| Min Signal to Noise Ratio | Min SNR, The signal is the value of the cwt matrix at the shortest length scale, the noise is the noise percentile of datapoints contained within a window around the identified signal |
| Noise Percentile | Used in Min SNR calculation |
| Gap Threshold | A ridge line is discontinued if there are more than Gap Threshold points without connecting a new relative maximum. |