elevOrGapClassif

classify the contig/chunk as 'gap' if the elevated region is less than 50
the length of the contig/chunk and otherwise classify as 'elevation'.

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

elevOrGapClassif function

<dl><dt>bestMatchList</dt>
<dd>A list containing pattern-match information associated with
all contigs/chunks classified by `ProActive()` pattern-matching</dd>
<dt>pileupSubset</dt>
<dd>A subset of the pileup that pertains only to the contig/chunk
currently being assessed.</dd></dl>

Arguments

Classifies partial elevation/gap pattern-matches — elevOrGapClassif

<dl>

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


<dt>pileupSubset</dt>
<dd>A subset of the pileup that pertains only to the contig/chunk
currently being assessed.</dd>

</dl>

elevOrGapClassif: Classifies partial elevation/gap pattern-matches

Description

Usage

Arguments