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Astrid Deschenes edited this page Mar 31, 2015 · 26 revisions

similaRpeak

Metrics to estimate the level of similarity between two ChIP profiles.

The metrics are:

  • RATIO_AREA: The ratio between the profile areas. The first profile is always divided by the second profile. NA is returned if minimal area threshold is not respected for at least one of the profiles.

  • DIFF_POS_MAX: The difference between the maximal peaks positions. The difference is always the first profile value minus the second profile value. NA is returned if minimal peak value is not respected. A profile can have more than one position with the maximum value. In that case, the median position is used. A threshold argument can be set to consider all positions within a certain range of the maximum value. A threshold argument can also be set to ensure that the distance between two maximum values is not too wide. When this distance is not respected, it is assumed that more than one peak is present in the profile and NA is returned.

  • RATIO_MAX_MAX: The ratio between the maximal peaks values in each profile. The first profile is always divided by the second profile. NA if minimal peak value threshold is not respected for at least one of the profiles.

  • RATIO_INTERSECT: The ratio between the intersection area and the total area of the two profiles. NA if minimal area threshold is not respected for the intersection area.

  • RATIO_NORMALIZED_INTERSECT: The ratio between the intersection area and the total area of two normalized profiles. The profiles are normalized by dividing them by their average value. NA if minimal area threshold is not respected for the intersection area.

  • SPEARMAN_CORRELATION: The Spearman's rho statistic between profiles.

Metrics

##How to do it…##

Demo: Comparison of 2 profiles

Use metagene package To extract ChIP-Seq profiles used as input in similaRpeak package

Authors

Astrid Louise Deschenes, Elsa Bernatchez, Charles Joly Beauparlant, Fabien Claude Lamaze, Rawane Samb, Pascal Belleau and Arnaud Droit.

See Arnaud Droit Lab website.

NOTE

To use this current development version, the use of the development version of the R6 package (>= 2.0) is mandatory.

License

This package and the underlying similaRpeak code are distributed under the Artistic license 2.0. You are free to use and redistribute this software.

For more information on Artistic 2.0 License see http://opensource.org/licenses/Artistic-2.0

Bugs/Feature requests

If you have any bugs or feature requests, let us know. Thanks!

Arnaud Droit Lab

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