fullElevGap

Builds full elevation/gap pattern-matches, shrinks the width, and collects
best match information

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

fullElevGap function

<dl><dt>pileupSubset</dt>
<dd>A subset of the pileup that pertains only to the contig/chunk
currently being assessed.</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>minSize</dt>
<dd>The minimum size (in bp) of elevation or gap patterns. Default is 10000.</dd>
<dt>maxSize</dt>
<dd>The maximum size (in bp) of elevation or gap patterns. Default is NA
(i.e. no maximum).</dd>
<dt>elevOrGap</dt>
<dd>Pattern-matching on 'elevation' or 'gap' pattern.</dd></dl>

Arguments

Controller function for full elevation/gap pattern-matching — fullElevGap

<dl>

<dt>pileupSubset</dt>
<dd>A subset of the pileup that pertains only to the contig/chunk
currently being assessed.</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>minSize</dt>
<dd>The minimum size (in bp) of elevation or gap patterns. Default is 10000.</dd>


<dt>maxSize</dt>
<dd>The maximum size (in bp) of elevation or gap patterns. Default is NA
(i.e. no maximum).</dd>


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

</dl>

fullElevGap: Controller function for full elevation/gap pattern-matching

Description

Usage

Arguments