classifSumm

Summarizes the list of pattern-matching classifications into a table.

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

classifSumm function

<dl><dt>pileup</dt>
<dd>A .txt file containing mapped sequencing read coverages averaged over
100 bp windows/bins.</dd>
<dt>bestMatchList</dt>
<dd>A list containing pattern-match information associated with
all contigs/chunks classified by `ProActive()` pattern-matching</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>mode</dt>
<dd>Either "genome" or "metagenome"</dd>
<dt>chunkSize</dt>
<dd>If `mode`="genome" OR if `mode`="metagenome" and `chunkContigs`=TRUE,
chunk the genome or contigs, respectively, into smaller subsets for pattern-matching.</dd></dl>

Arguments

Summarizes pattern-matching results — classifSumm

<dl>

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


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


<dt>chunkSize</dt>
<dd>If `mode`="genome" OR if `mode`="metagenome" and `chunkContigs`=TRUE,
chunk the genome or contigs, respectively, into smaller subsets for pattern-matching.</dd>

</dl>

classifSumm: Summarizes pattern-matching results

Description

Usage

Arguments