fullElevGap: Controller function for full elevation/gap pattern-matching

In ProActive: Detect Elevations and Gaps in Mapped Sequencing Read Coverage

Controller function for full elevation/gap pattern-matching

Description

Builds full elevation/gap pattern-matches, shrinks the width, and collects best match information

Usage

fullElevGap(pileupSubset, windowSize, minSize, maxSize, elevOrGap)

Arguments

pileupSubset	A subset of the pileup that pertains only to the contig/chunk currently being assessed.
windowSize	The number of basepairs to average read coverage values over. Options are 100, 200, 500, 1000 ONLY. Default is 1000.
minSize	The minimum size (in bp) of elevation or gap patterns. Default is 10000.
maxSize	The maximum size (in bp) of elevation or gap patterns. Default is NA (i.e. no maximum).
elevOrGap	Pattern-matching on 'elevation' or 'gap' pattern.

ProActive documentation built on April 4, 2025, 12:58 a.m.