collectBestMatchInfo

Make a list containing the match-score, min and max pattern-match values,
the start and stop positions of the elevated or gapped region, the elevation
ratio and the 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

collectBestMatchInfo function

<dl><dt>pattern</dt>
<dd>A vector containing the values associated with the pattern-match</dd>
<dt>pileupSubset</dt>
<dd>A subset of the pileup that pertains only to the contig/chunk
currently being assessed.</dd>
<dt>elevOrGap</dt>
<dd>Pattern-matching on 'elevation' or 'gap' pattern.</dd>
<dt>leftRightFull</dt>
<dd>'Left' or'Right' partial gap/elevation pattern or full
elevation/gap pattern.</dd></dl>

Arguments

Collect information regarding the pattern-match — collectBestMatchInfo

<dl>

<dt>pattern</dt>
<dd>A vector containing the values associated with the pattern-match</dd>


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


<dt>elevOrGap</dt>
<dd>Pattern-matching on 'elevation' or 'gap' pattern.</dd>


<dt>leftRightFull</dt>
<dd>'Left' or'Right' partial gap/elevation pattern or full
elevation/gap pattern.</dd>

</dl>

collectBestMatchInfo: Collect information regarding the pattern-match

Description

Usage

Arguments