partialElevGap: Controller function for partial elevation/gap...

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

Controller function for partial elevation/gap pattern-matching

Description

Builds partial elevation/gap pattern-match for patterns going off both the left and right sides of the contig/chunk, shrinks the width, and collects best match information

Usage

partialElevGap(pileupSubset, windowSize, minSize, maxSize)

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).

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