version 0.8.5
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Davide Cittaro
May 7, 2011, 3:24:49 AM5/7/11
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Hi all,
I've recently uploaded version 0.8.5 of dspchip. I've introduced the possibility to perform local and global thresholding. Global thresholding is the default, a threshold is calculated (with Otsu's method or estimating the MAD) using all the chromosome data. If local thresholding is specified, thresholds will be calculated on chromosome chunks and a 3rd order spline will be used to interpolate a threshold for each point along the chromosome. To use this feature, just add 'local' keyword to threshold definition, separating it with a comma (i.e. '--threshold=local,otsu')
Besides, I've completely removed some leftovers (baselines, FFT).
Spoiler alert:
Next step will be the introduction of Wiener filtering to reconstruct degraded data.
I've recently uploaded version 0.8.5 of dspchip. I've introduced the possibility to perform local and global thresholding. Global thresholding is the default, a threshold is calculated (with Otsu's method or estimating the MAD) using all the chromosome data. If local thresholding is specified, thresholds will be calculated on chromosome chunks and a 3rd order spline will be used to interpolate a threshold for each point along the chromosome. To use this feature, just add 'local' keyword to threshold definition, separating it with a comma (i.e. '--threshold=local,otsu')
Besides, I've completely removed some leftovers (baselines, FFT).
Spoiler alert:
Next step will be the introduction of Wiener filtering to reconstruct degraded data.
d
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Davide Cittaro
daweo...@gmail.com
http://sites.google.com/site/davidecittaro/
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