patternTranslator

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.

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

patternTranslator function

<dl><dt>contigCov</dt>
<dd>The read coverages that pertain to the pileupSubset</dd>
<dt>bestMatchInfo</dt>
<dd>The information associated with the current best pattern-match
for the contig/chunk 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>pattern</dt>
<dd>A vector containing the values associated with the pattern-match</dd>
<dt>elevOrGap</dt>
<dd>Pattern-matching on 'elevation' or 'gap' pattern.</dd></dl>

Arguments

Full elevation/gap pattern translator — patternTranslator

<dl>

<dt>contigCov</dt>
<dd>The read coverages that pertain to the pileupSubset</dd>


<dt>bestMatchInfo</dt>
<dd>The information associated with the current best pattern-match
for the contig/chunk 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>pattern</dt>
<dd>A vector containing the values associated with the pattern-match</dd>


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

</dl>

patternTranslator: Full elevation/gap pattern translator

Description

Usage

Arguments