PeakSegJointHeuristicStep2: PeakSegJointHeuristicStep2

In PeakSegJoint: Joint Peak Detection in Several ChIP-Seq Samples

PeakSegJointHeuristicStep2

Description

Run the first and second steps of the PeakSegJoint fast heuristic optimization algorithm. Step2 the SearchNearPeak subroutine described in the JointZoom Algorithm of arXiv:1506.01286, and it is guaranteed to return feasible segmentations (seg1 < seg2 > seg3). NB: this function is only for testing the C code against the R implementation (search tests/testthat/*.R files for Step2). For real data see PeakSegJointSeveral.

Usage

PeakSegJointHeuristicStep2(profiles, 
    bin.factor = 2L)

Arguments

profiles	List of data.frames with columns chromStart, chromEnd, count, or single data.frame with additional column sample.id.
bin.factor	Size of bin pyramid. Bigger values result in slower computation.

Value

List of model fit results, which can be passed to ConvertModelList for easier interpretation.

Author(s)

Toby Dylan Hocking

PeakSegJoint documentation built on April 25, 2023, 9:12 a.m.