diffPosMaxMethod: Difference between two profiles maximal peaks positions

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

Description

Calculate and return the difference between two profiles maximal peaks positions. The difference is always the first profile value (profile1 parameter) minus the second profile value (profile2 parameter). When more than one maximual peak is present in one profile, the mediane of the position is calculated and used as the maximal peak position. If one threshold is not respected, the function returns NA.

Usage

diffPosMaxMethod(profile1, profile2, threshold = 1, thresholdDist = 100,
  tolerance = 0.01)

Arguments

profile1	a vector of numeric values, the first profile containing the alignment depth for each position. The profile1 and profile2 should have the same length.
profile2	a vector of numeric values, the second profile containing the alignment depth for each position. The profile1 and profile2 should have the same length.
threshold	a numeric, the minimum peak value accepted to calculate the metric. Default = 1.
thresholdDist	a numeric, the maximum distance accepted between two maximum peaks positions in the same profile. Default = 100.
tolerance	a numeric, the maximum variation accepted on the maximum value to consider a position as a peak position. The tolerance must

Value

The calculated ratio or NA if not all thresholds are respected.

Author(s)

Astrid Deschenes, Elsa Bernatchez

See Also

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

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