refineRegion: Refine the selected region by using an iterative process.

In ArnaudDroitLab/consensusSeekeR: Detection of consensus regions inside a group of experiences using genomic positions and genomic ranges

Description

Find regions sharing the same features for a minimum number of experiments using called peaks of signal enrichment based on pooled, normalized data (mainly coming from narrowPeak files). Tje analysis is limited to one chromosome. The peaks and narrow peaks are used to identify the consensus regions. The minimum number of experiments that must have at least on peak in a region so that it is retained as a consensus region is specified by user, as well as the size of mining regions.

Usage

refineRegion(peaks, setPeaks, extendingSize, region_width, currentPeak)

Arguments

peaks	a GRanges containing all peaks from the current analysis sorted by position.
setPeaks	a GRanges containing the peaks present in the current selected region.
extendingSize	a numeric value indicating the size of padding at each side of the peaks median position to create the consensus region. The minimum size of the consensu region will be equal to twice the value of the extendingSize parameter. The size of the extendingSize must be a positive integer.
region_width	a numeric value indicating the size of the region which is equivalent to twice the extendingSize.
currentPeak	a GRanges with 1 range containing the information about the current peak used as the starting point for the selected region.

Value

an object of class "commonFeatures".

Author(s)

Astrid Deschenes

ArnaudDroitLab/consensusSeekeR documentation built on Feb. 6, 2020, 6:45 p.m.