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View Code? Open in Web Editor NEWBioconductor Package - Metrics to estimate the level of similarity between two ChIP-Seq profiles
Home Page: http://bioconductor.org/packages/similaRpeak/
Bioconductor Package - Metrics to estimate the level of similarity between two ChIP-Seq profiles
Home Page: http://bioconductor.org/packages/similaRpeak/
Not all similarity() parameters prerequisites are tested.
etc....
BiocCheck() must pass on package.
The current DIFF_POS_MAX metric is not appropriate when more than 1 peak is present.
The modifications includes:
1- Add tolerance value, in % of the max value, which will allow positions close to max value to be considered as max position.
2- Add threshold for the max value so the metric is not calculated when the max is low. Default : >0. When threshold not reached, NA value is returned.
3- Add threshold on position distance for 2 peak value to be considered as coming from a single peak. Default value = 100. When threshold not respected, NA value is returned.
4- When all threshold are respected, use the median position to calculate the position of the peak when more than one position present.
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