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BinMat (version 0.1.5)

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

Description

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: . The GUI version of this package is available on the R Shiny online server at: 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) , and an ISSR dataset of Nymphaea specimens from Reid et. al. (2021) . The authors of these publications are thanked for allowing the use of their data.

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Version

Install

install.packages('BinMat')

Monthly Downloads

247

Version

0.1.5

License

GPL-3

Maintainer

Clarke van Steenderen

Last Published

March 6th, 2022

Functions in BinMat (0.1.5)

peaks.consolidated

Calculates peak numbers for a consolidated data set (total, maximum, and minimum).
upgma

Draws a hierarchical clustering tree (UPGMA).
shepard

Creates a shepard plot.
scree

Draws a scree plot.
peaks.original

Calculates peak numbers for the data set with all replicates (total, maximum, and minimum).
BinMatInput_reps

Example input data containing a binary matrix comprising replicate pairs
BinMatInput_ordination

Example input data containing a consolidated binary matrix with groups
check.data

Checks binary matrix for unwanted characters.
consolidate

Consolidates replicate pairs in a binary matrix.
peak.remove

Removes samples with peaks equal to or less than a specified threshold value.
group.names

Outputs group names specified in the input file for the creation of an nMDS plot.
errors

Calculates Jaccard and Euclidean error rates.
nymphaea

Example input file of Nymphaea ISSR data, taken from Reid et. al. (2021). This dataset has already been consolidated, and can be used as input for the generation of an nMDS plot. The paper can be found here: <https://www.sciencedirect.com/science/article/pii/S0304377021000218>
bunias_orientalis

Example input file of Bunias orientalis AFLP data, taken from Tewes et. al. (2017). This dataset has already been consolidated, and can be used as input for the generation of an nMDS plot. The paper can be found here: <https://besjournals.onlinelibrary.wiley.com/doi/full/10.1111/1365-2745.12869>
nmds

Creates a non-metric multidimensional scaling plot (nMDS).