fullElevGapShrink

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

internal

Automate the detection of gaps and elevations in mapped sequencing
read coverage using a 2D pattern-matching algorithm. 'ProActive' detects, characterizes
and visualizes read coverage patterns in both genomes and metagenomes. Optionally,
users may provide gene annotations associated with their genome or metagenome
in the form of a .gff file. In this case, 'ProActive' will generate an additional
output table containing the gene annotations found within the detected regions of gapped
and elevated read coverage. Additionally, users can search for gene
annotations of interest in the output read coverage plots.

Jessie Maier

ProActive

Detect Elevations and Gaps in Mapped Sequencing Read Coverage

Manuel Kleiner

fullElevGapShrink function

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

Arguments

Shrink the width of full elevation and gap patterns — fullElevGapShrink

<dl>

<dt>minCov</dt>
<dd>The minimum value of the pattern-match vector.</dd>


<dt>windowSize</dt>
<dd>The number of basepairs to average read coverage values over.
Options are 100, 200, 500, 1000 ONLY. Default is 1000.</dd>


<dt>maxCov</dt>
<dd>The maximum value of the pattern-match vector.</dd>


<dt>elevLength</dt>
<dd>Length of the elevated/gapped pattern-match region.</dd>


<dt>nonElev</dt>
<dd>Length of the non-elevated/gapped pattern-match region.</dd>


<dt>bestMatchInfo</dt>
<dd>The information associated with the current best pattern-match
for the contig/chunk being assessed.</dd>


<dt>pileupSubset</dt>
<dd>A subset of the pileup that pertains only to the contig/chunk
currently being assessed.</dd>


<dt>minSize</dt>
<dd>The minimum size (in bp) of elevation or gap patterns. Default is 10000.</dd>


<dt>elevOrGap</dt>
<dd>Pattern-matching on 'elevation' or 'gap' pattern.</dd>

</dl>

fullElevGapShrink: Shrink the width of full elevation and gap patterns

Description

Usage

Arguments