Package: BinMat 0.1.5

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

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: <https://www.sciencedirect.com/science/article/pii/S1049964420306538>. 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) <https://besjournals.onlinelibrary.wiley.com/doi/full/10.1111/1365-2745.12869>, and an ISSR dataset of Nymphaea specimens from Reid et. al. (2021) <https://www.sciencedirect.com/science/article/pii/S0304377021000218> . The authors of these publications are thanked for allowing the use of their data.

Authors:Clarke van Steenderen [aut, cre]

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BinMat.pdf |BinMat.html✨
BinMat/json (API)

# Install 'BinMat' in R:
install.packages('BinMat', repos = c('https://clarkevansteenderen.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Datasets:
  • BinMatInput_ordination - Example input data containing a consolidated binary matrix with groups
  • BinMatInput_reps - Example input data containing a binary matrix comprising replicate pairs
  • bunias_orientalis - Example input file of Bunias orientalis AFLP data
  • 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>

On CRAN:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

2.00 score 3 scripts 244 downloads 11 exports 69 dependencies

Last updated 3 years agofrom:ac2c0bdb30. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 29 2024
R-4.5-winOKOct 29 2024
R-4.5-linuxOKOct 29 2024
R-4.4-winOKOct 29 2024
R-4.4-macOKOct 29 2024
R-4.3-winOKOct 29 2024
R-4.3-macOKOct 29 2024

Exports:check.dataconsolidateerrorsgroup.namesnmdspeak.removepeaks.consolidatedpeaks.originalscreeshepardupgma

Dependencies:abindbackportsbootbroomcarcarDataclicolorspacecorrplotcowplotcpp11DerivdoBydplyrfansifarverFormulagenericsggplot2ggpubrggrepelggsciggsignifgluegridExtragtableisobandlabelinglatticelifecyclelme4magrittrMASSMatrixMatrixModelsmgcvmicrobenchmarkminqamodelrmunsellnlmenloptrnnetnumDerivpbkrtestpillarpkgconfigpolynompurrrpvclustquantregR6RColorBrewerRcppRcppEigenrlangrstatixscalesSparseMstringistringrsurvivaltibbletidyrtidyselectutf8vctrsviridisLitewithr

BinMat: Processes Binary Data Obtained from Fragment Analysis

Clarke van Steenderen

Rendered fromBinMat.Rmdusingknitr::rmarkdownon Oct 29 2024.

Last update: 2022-03-06
Started: 2020-02-29

Readme and manuals

Help Manual

Help pageTopics
Example input data containing a consolidated binary matrix with groupsBinMatInput_ordination
Example input data containing a binary matrix comprising replicate pairsBinMatInput_reps
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>bunias_orientalis
Checks binary matrix for unwanted characters.check.data
Consolidates replicate pairs in a binary matrix.consolidate
Calculates Jaccard and Euclidean error rates.errors
Outputs group names specified in the input file for the creation of an nMDS plot.group.names
Creates a non-metric multidimensional scaling plot (nMDS).nmds
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>nymphaea
Removes samples with peaks equal to or less than a specified threshold value.peak.remove
Calculates peak numbers for a consolidated data set (total, maximum, and minimum).peaks.consolidated
Calculates peak numbers for the data set with all replicates (total, maximum, and minimum).peaks.original
Draws a scree plot.scree
Creates a shepard plot.shepard
Draws a hierarchical clustering tree (UPGMA).upgma