| Title: | Linkmapper: A GUI for Linkage Mapping and QTL Visualisation |
|---|---|
| Description: | A Shiny web application that wraps the 'onemap' R package to let users perform linkage mapping and QTL visualisation on biparental mapping populations (F2 intercross and backcross) without writing any code. Provides a graphical workflow for data upload, segregation distortion testing, two-point linkage analysis, marker grouping, linkage group ordering, and final linkage map generation and download. Designed for students and researchers in molecular genetics and plant breeding who require a reproducible, open-source alternative to commercial linkage mapping software. |
| Authors: | Ebenezer Ogoe [aut, cre], Michael Obeng [ctb], Barnie Stephen Amoako [ctb] |
| Maintainer: | Ebenezer Ogoe <[email protected]> |
| License: | MIT + file LICENSE |
| Version: | 0.1.0 |
| Built: | 2026-06-22 23:22:05 UTC |
| Source: | https://github.com/ebenogoe/linkmapper |
Performs two-point linkage analysis with onemap::rf_2pts() and groups
markers into linkage groups with onemap::group(). This is Module 2 of
the Linkmapper analytical workflow.
group_markers(onemap_obj, lod = 3, max_rf = 0.5, map_fun = "kosambi")group_markers(onemap_obj, lod = 3, max_rf = 0.5, map_fun = "kosambi")
onemap_obj |
An |
lod |
Numeric. LOD score threshold for declaring linkage. Passed to
|
max_rf |
Numeric in [0, 0.5]. Maximum recombination frequency for
declaring linkage. Passed to |
map_fun |
Character. Mapping function. One of |
To obtain a data-suggested LOD threshold instead of supplying a fixed value,
call onemap::suggest_lod() on the onemap object first and pass the
result as lod.
An object of class "sequence" (as returned by onemap::group())
with field $n.groups giving the number of linkage groups detected.
## Not run: f2data <- validate_lm_file("path/to/mydata.txt") # Use a fixed LOD threshold lgs <- group_markers(f2data, lod = 3, max_rf = 0.5) lgs$n.groups # Or let onemap suggest the LOD suggested <- onemap::suggest_lod(f2data) lgs <- group_markers(f2data, lod = suggested, max_rf = 0.5) ## End(Not run)## Not run: f2data <- validate_lm_file("path/to/mydata.txt") # Use a fixed LOD threshold lgs <- group_markers(f2data, lod = 3, max_rf = 0.5) lgs$n.groups # Or let onemap suggest the LOD suggested <- onemap::suggest_lod(f2data) lgs <- group_markers(f2data, lod = suggested, max_rf = 0.5) ## End(Not run)
Launches the Linkmapper GUI in the default web browser (or RStudio Viewer). The application provides a point-and-click workflow for linkage mapping and QTL visualisation on biparental mapping populations using the onemap package as the computational back-end.
run_linkmapper(...)run_linkmapper(...)
... |
Additional arguments passed to |
Does not return a value; called for its side effect of launching the Shiny application. The function blocks until the app is stopped.
## Not run: # Launch on a random available port and open in the default browser run_linkmapper() # Launch on a specific port without opening a browser run_linkmapper(port = 4321, launch.browser = FALSE) ## End(Not run)## Not run: # Launch on a random available port and open in the default browser run_linkmapper() # Launch on a specific port without opening a browser run_linkmapper(port = 4321, launch.browser = FALSE) ## End(Not run)
Attempts to read a MAPMAKER-format text file using
onemap::read_mapmaker(), then validates that the result is a non-empty
onemap object. This is the first step in the Linkmapper analytical
workflow; all downstream functions expect the object this function returns.
validate_lm_file(path)validate_lm_file(path)
path |
Character string. Path to the |
An onemap object as returned by onemap::read_mapmaker().
Stops with an informative error if (a) the file cannot be found,
(b) the extension is not .txt, (c) onemap::read_mapmaker() throws
an error, (d) the result is not an onemap object, or (e) the dataset
contains zero individuals or zero markers.
## Not run: f2data <- validate_lm_file("path/to/mydata.txt") f2data # prints onemap summary: n individuals, n markers, cross type ## End(Not run)## Not run: f2data <- validate_lm_file("path/to/mydata.txt") f2data # prints onemap summary: n individuals, n markers, cross type ## End(Not run)