SpearmanCorrelation: SpearmanCorrelation class

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

Description

An object which is a interface to calculate the Spearman's

The SpearmanCorrelation object is needed to calculate the ratio between the peaks values between two profiles. A threshold and the two profiles are set during the SpearmanCorrelation object creation. If different threshold or profiles are needed, the calculateMetric function should be used, with the new profiles and threshold passed as arguments to update those values inside the SpearmanCorrelation object.

The threshold is the minimum standard deviation of the profile accepted to calculate a ratio.

Usage

SpearmanCorrelation

Format

An object of class R6ClassGenerator of length 24.

Value

The SpearmanCorrelation$new function returns a SpearmanCorrelation object which contains the information about the two profiles. It can be used, as many times needed, to calculate the specified metric.

Constructor

Create a SpearmanCorrelation object.

SpearmanCorrelation$new(profile1, profile2, threshold = 1e-8)

The threshold is the minimum standard deviation of the profile accepted to calculate a ratio. Default = 1e-8

The SpearmanCorrelation object inherites those functions:

• getMetric A function that returns the value of the calculated metric

• getInfo A function that returns a description of the metric with the metric value.

• getType A function that returns the unique name associated to this metric

• calculateMetric A function that modifies the values of the two profiles and the threshold. The new values (profile1, profile2) are passed as arguments.

Author(s)

Astrid Deschenes

See Also

• MetricFactory for using a interface to calculate all available metrics separately or togheter.

similaRpeak documentation built on Nov. 8, 2020, 6:56 p.m.