geneAnnotationPlot

Plot read coverage and location of gene annotations that match the keywords and
search criteria for contig/chunk currently being assessed

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

geneAnnotationPlot function

<dl><dt>geneAnnotSubset</dt>
<dd>Subset of gene annotations to be plotted</dd>
<dt>keywords</dt>
<dd>The key-word(s) used for the search.</dd>
<dt>pileupSubset</dt>
<dd>A subset of the pileup associated with the contig/chunk being assessed</dd>
<dt>colIdx</dt>
<dd>The column index 'gene' or 'product' column</dd>
<dt>startbpRange</dt>
<dd>The basepair at which the search is started if a 'specific' search is used</dd>
<dt>endbpRange</dt>
<dd>The basepair at which the search is ended if a 'specific' search is used</dd>
<dt>elevRatio</dt>
<dd>The maximum/minimum values of the pattern-match</dd>
<dt>pattern</dt>
<dd>The pattern-match information associated with the contig/chunk being assessed</dd>
<dt>windowSize</dt>
<dd>The number of basepairs to average read coverage values over.</dd></dl>

Arguments

Gene annotation plot — geneAnnotationPlot

<dl>

<dt>geneAnnotSubset</dt>
<dd>Subset of gene annotations to be plotted</dd>


<dt>keywords</dt>
<dd>The key-word(s) used for the search.</dd>


<dt>pileupSubset</dt>
<dd>A subset of the pileup associated with the contig/chunk being assessed</dd>


<dt>colIdx</dt>
<dd>The column index 'gene' or 'product' column</dd>


<dt>startbpRange</dt>
<dd>The basepair at which the search is started if a 'specific' search is used</dd>


<dt>endbpRange</dt>
<dd>The basepair at which the search is ended if a 'specific' search is used</dd>


<dt>elevRatio</dt>
<dd>The maximum/minimum values of the pattern-match</dd>


<dt>pattern</dt>
<dd>The pattern-match information associated with the contig/chunk being assessed</dd>


<dt>windowSize</dt>
<dd>The number of basepairs to average read coverage values over.</dd>

</dl>

geneAnnotationPlot: Gene annotation plot

Description

Usage

Arguments