linkChunks

Detect partial gap/elevation pattern matches that fall on the edges of chunked
genomes/contigs that may be part of the same pattern prior to chunking

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

linkChunks function

<dl><dt>bestMatchList</dt>
<dd>A list containing pattern-match information associated with
all contigs/chunks classified by `ProActive()` pattern-matching</dd>
<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>mode</dt>
<dd>Either "genome" or "metagenome"</dd>
<dt>verbose</dt>
<dd>TRUE or FALSE. Print progress messages to console. Default is TRUE.</dd></dl>

Arguments

Link pattern-matches on contig/genome chunks — linkChunks

<dl>

<dt>bestMatchList</dt>
<dd>A list containing pattern-match information associated with
all contigs/chunks classified by `ProActive()` pattern-matching</dd>


<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>mode</dt>
<dd>Either "genome" or "metagenome"</dd>


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

</dl>

linkChunks: Link pattern-matches on contig/genome chunks

Description

Usage

Arguments