patternMatcher

Creates the pileupSubset, representative of one contig/chunk, used as input for
each individual pattern-matching function. After the information associated with
the best match for each pattern is obtained, the pattern-match with the lowest
mean absolute difference (match-score) is used for classification.

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

patternMatcher function

<dl><dt>pileup</dt>
<dd>A .txt file containing mapped sequencing read coverages averaged over
100 bp windows/bins.</dd>
<dt>windowSize</dt>
<dd>The number of basepairs to average read coverage values over.</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>mode</dt>
<dd>Either "genome" or "metagenome".</dd>
<dt>minContigLength</dt>
<dd>The minimum contig/chunk size (in bp) to perform pattern-matching
on. Default is 25000.</dd>
<dt>verbose</dt>
<dd>TRUE or FALSE. Print progress messages to console. Default is TRUE.</dd></dl>

Arguments

Controller function for pattern-matching — patternMatcher

<dl>

<dt>pileup</dt>
<dd>A .txt file containing mapped sequencing read coverages averaged over
100 bp windows/bins.</dd>


<dt>windowSize</dt>
<dd>The number of basepairs to average read coverage values over.</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>mode</dt>
<dd>Either "genome" or "metagenome".</dd>


<dt>minContigLength</dt>
<dd>The minimum contig/chunk size (in bp) to perform pattern-matching
on. Default is 25000.</dd>


<dt>verbose</dt>
<dd>TRUE or FALSE. Print progress messages to console. Default is TRUE.</dd>

</dl>

patternMatcher: Controller function for pattern-matching

Description

Usage

Arguments