similaRpeak-package {similaRpeak} | R Documentation

## similaRpeak: Metrics to estimate a level of similarity between two ChIP-Seq profiles

### Description

This package is calculating six differents metrics to estimate a level of similarity between two ChIP-Seq profiles.

### Details

The `similarity` function calculates six differents metrics:

- RATIO_AREA: The ratio between the areas. The larger value is always divided by the smaller value.

- DIFF_POS_MAX: The difference between the maximal peaks positions. The difference is always a positive value.

- RATIO_MAX_MAX: The ratio between the maximal peaks values. The larger value is always divided by the smaller value.

- RATIO_INTERSECT: The ratio between the intersection area and the total area.

- RATIO_NORMALIZED_INTERSECT: The ratio between the intersection area and the total area of two normalized profiles. The profiles are normalized by divinding them by their average value.

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

The function `similarity` also reports basic information about each ChIP profile such as the number of positions, the area, the maximum value and the position of the maximum value.

To learn more about similaRpeak package see: https://github.com/adeschen/similaRpeak/wiki

### Author(s)

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

Maintainer: Astrid Deschenes <adeschen@hotmail.com>

### See Also

- `MetricFactory` for using a interface to calculate all available metrics separately.

- `similarity` for calculating all available metrics between two ChIP-Seq profiles.

[Package similaRpeak version 1.12.0 Index]