fullElevGapShrink {ProActive} | R Documentation |
Shrink the width of full elevation and gap patterns
Description
Remove values from gapped/elevated region in the pattern-match vector until it reaches the 'minSize'
Usage
fullElevGapShrink(
minCov,
windowSize,
maxCov,
elevLength,
nonElev,
bestMatchInfo,
pileupSubset,
minSize,
elevOrGap
)
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. |
elevOrGap |
Pattern-matching on 'elevation' or 'gap' pattern. |
[Package ProActive version 0.1.0 Index]