| Type: | Package |
| Title: | A Shiny Application for Allele Binning in Microsatellite Markers |
| Version: | 1.0.0 |
| Description: | Provides allele binning functionality for SSR/microsatellite markers using least-squares minimization (Idury & Cardon (1997) <doi:10.1101/gr.7.11.1104>). Includes a 'Shiny' application for interactive use, summary statistics, and visualization. |
| License: | GPL-3 |
| Encoding: | UTF-8 |
| Imports: | shiny, readxl, stats, utils, openxlsx |
| Suggests: | testthat (≥ 3.0.0), roxygen2 |
| Config/roxygen2/version: | 8.0.0 |
| Config/testthat/edition: | 3 |
| URL: | https://github.com/vpprasanth/AlleloBin |
| BugReports: | https://github.com/vpprasanth/AlleloBin/issues |
| NeedsCompilation: | no |
| Packaged: | 2026-08-29 08:07:51 UTC; vppra |
| Author: | VP Prasanth [aut, cre], Subhash Chandra [aut], DA Hoisington [aut], B Jayashree [aut] |
| Maintainer: | VP Prasanth <prasanth.stat@gmail.com> |
| Repository: | CRAN |
| Date/Publication: | 2026-09-10 09:10:02 UTC |
Run AlleloBin Shiny App
Description
Launches the Shiny application for allele binning.
Usage
AlleloBin()
Value
No return value, launches 'Shiny' app
Allele Binning Function
Description
This function bins observed SSR allele sizes into discrete allele classes using repeat length information (Idury & Cardon, 1997).
Usage
allele_binning(data, repeat_lengths, ploidy = 2, progress = FALSE)
Arguments
data |
A data.frame with columns: Marker, Genotype, Allele1...AlleleN |
repeat_lengths |
A numeric vector of repeat lengths (same order as markers) |
ploidy |
Integer, number of alleles per genotype (default = 2) |
progress |
Logical, whether to update a Shiny progress bar |
Value
A list of results per marker: min/max allele, bins, frequencies
Example Data
Description
Example SSR allele dataset ('data.txt') and repeat length file ('info.txt') included with the package.
Details
References Idury, R.M. & Cardon, L.R. (1997). A Simple Method for Automated Allele Binning in Microsatellite Markers. Genome Research, 11:1104–1109.
Value
A data.frame with example SSR allele data
Examples
datafile <- system.file("extdata", "data.txt", package = "AlleloBin")
infofile <- system.file("extdata", "repeat_length.txt", package = "AlleloBin")
data <- read.table(datafile, header = FALSE)
info <- read.table(infofile, header = FALSE)
repeat_lens <- as.numeric(info[[1]])
allele_binning(data, repeat_lens, ploidy = 2)
Save AlleloBin results to Excel
Description
Utility function to export allele binning results into an Excel workbook. Each marker gets its own worksheet containing bin summary, allele calls, and marker summary with strict decimal formatting.
Usage
save_results(results, file)
Arguments
results |
List of marker results from allele_binning() |
file |
Output Excel file path |
Value
None (writes Excel file to disk)
Examples
xlsx_file <- system.file("extdata", "data.xlsx", package = "AlleloBin")
repeat_file <- system.file("extdata", "repeat_length.xlsx", package = "AlleloBin")
data_xlsx <- openxlsx::read.xlsx(xlsx_file)
# Ensure repeat_length is numeric vector, not data frame
repeat_length <- as.numeric(openxlsx::read.xlsx(repeat_file)[[1]])
results <- allele_binning(data_xlsx, repeat_length, ploidy = 2)
save_results(results, file.path(tempdir(), "AlleloBin_Output.xlsx"))