partialElevGapShrink: Shrink the width of partial elevation and gap patterns

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

Shrink the width of partial elevation and gap patterns

Description

Remove values from gapped/elevated region in the pattern-match vector until it reaches the 'minSize'.

Usage

partialElevGapShrink(
  minCov,
  windowSize,
  maxCov,
  elevLength,
  nonElev,
  bestMatchInfo,
  pileupSubset,
  minSize,
  leftOrRight
)

Arguments

minCov	The minimum value of the pattern-match vector.
windowSize	The number of basepairs to average read coverage values over. Options are 100, 200, 500, 1000 ONLY. Default is 1000.
maxCov	The maximum value of the pattern-match vector.
elevLength	Length of the elevated/gapped pattern-match region.
nonElev	Length of the non-elevated/gapped pattern-match region.
bestMatchInfo	The information associated with the current best pattern-match for the contig/chunk being assessed.
pileupSubset	A subset of the pileup that pertains only to the contig/chunk currently being assessed.
minSize	The minimum size (in bp) of elevation or gap patterns. Default is 10000.
leftOrRight	'Left' or 'Right' partial gap/elevation pattern.

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