patternTranslator: Full elevation/gap pattern translator

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

Full elevation/gap pattern translator

Description

Translates full elevation/gap patterns across contigs/chunks 1000bp at a time. Translation stops when the elevation pattern is 5000bp from the end of the contig/chunk.

Usage

patternTranslator(contigCov, bestMatchInfo, windowSize, pattern, elevOrGap)

Arguments

contigCov	The read coverages that pertain to the pileupSubset
bestMatchInfo	The information associated with the current best pattern-match for the contig/chunk being assessed.
windowSize	The number of basepairs to average read coverage values over. Options are 100, 200, 500, 1000 ONLY. Default is 1000.
pattern	A vector containing the values associated with the pattern-match
elevOrGap	Pattern-matching on 'elevation' or 'gap' pattern.

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