peak.remove

Removes samples with a peak number less than a specified value.

A molecular genetics tool that processes binary data from fragment analysis. It consolidates replicate sample pairs, outputs summary statistics, and produces hierarchical clustering trees and nMDS plots. This package was developed from the publication available here: <doi:10.1016/j.biocontrol.2020.104426>. The GUI version of this package is available on the R Shiny online server at: <https://clarkevansteenderen.shinyapps.io/BINMAT/> or it is accessible via GitHub by typing: shiny::runGitHub("BinMat", "clarkevansteenderen") into the console in R. Two real-world datasets accompany the package: an AFLP dataset of Bunias orientalis samples from Tewes et. al. (2017) <doi:10.1111/1365-2745.12869>, and an ISSR dataset of Nymphaea specimens from Reid et. al. (2021) <doi:10.1016/j.aquabot.2021.103372>. The authors of these publications are thanked for allowing the use of their data.

Clarke van Steenderen

BinMat

Processes Binary Data Obtained from Fragment Analysis (Such as
AFLPs, ISSRs, and RFLPs)

peak.remove function

<dl><dt>x</dt>
<dd>Binary matrix - consolidated or original.</dd>
<dt>thresh</dt>
<dd>Peak threshold value for removal.</dd></dl>

Arguments

Removes samples with peaks equal to or less than a specified threshold value. — peak.remove

<dl>

<dt>x</dt>
<dd>Binary matrix - consolidated or original.</dd>


<dt>thresh</dt>
<dd>Peak threshold value for removal.</dd>

</dl>

peak.remove: Removes samples with peaks equal to or less than a specified threshold value.

Description

Usage

Value

Arguments

Examples