Linkmapper

Linkmapper builds genetic linkage maps and locates QTL in F2 intercross, backcross and recombinant inbred line populations, without code. It is a point-and-click interface to onemap and R/qtl, with interactive maps, a report, and an R script that reproduces each analysis.

Hosted app: https://ebenogoe.shinyapps.io/linkmapper/

Linkage map with QTL intervals on the F2 demo

Workflow

  1. Load data. MAPMAKER or onemap raw genotype files, with traits in the file or from a separate CSV.
  2. Quality control. Missing data per marker and individual; chi-square segregation tests with Bonferroni correction; marker filters.
  3. Linkage groups. Two-point recombination fractions and LOD scores; grouping by LOD and maximum recombination fraction, with a suggested LOD threshold.
  4. Marker order. RECORD, RCD, unidirectional growth or seriation; Kosambi or Haldane distances; recombination-fraction heatmaps per group.
  5. Linkage map. Interactive map with positions and group summaries; PNG, SVG, PDF, CSV, Excel and MapChart exports.
  6. QTL mapping. Interval mapping (Haley-Knott, EM or imputation) or composite interval mapping; permutation thresholds; 1.5-LOD support intervals, variance explained and effects.
  7. Export. Self-contained HTML report, R script and session file.

Accepted data formats

Population Header line Genotype codes
F2 intercross data type f2 intercross A, H, B; C (not BB), D (not AA); - missing
Backcross data type f2 backcross A, H; - missing
RIL, selfing data type ri self A, B; - missing
RIL, sib mating data type ri sib A, B; - missing

Screenshots
Quality control Marker order
QTL mapping Export

Installation

install.packages("linkmapper", repos = c("https://ebenogoe.r-universe.dev", "https://cloud.r-project.org"))
linkmapper::run_app()

run_linkmapper(), validate_lm_file() and group_markers() from version 0.1 still work.

The analysis is also available as functions:

library(linkmapper)
d <- read_cross("my_population.raw")
d <- filter_markers(d, max_missing = 0.25)
g <- linkage_groups(d)
m <- order_groups(g, "record")
r <- scan_qtl(build_cross(d, m), n_perm = 1000)
plot_linkage_map(m, r)

Demo data

linkmapper_demo() loads the simulated F2, backcross and RIL examples shipped with onemap, and the 20-individual F2 file from the 2022 Linkmapper.

History

Linkmapper was created in 2022 at the Kwame Nkrumah University of Science and Technology (KNUST) by Ebenezer Ogoe, Michael Obeng and Stephen Amoako. Version 0.2 (2026) is a rewrite as an R package with backcross and RIL support, R/qtl-based QTL mapping, an interactive map and reproducible exports. See NEWS.md.

Citation

Run citation("linkmapper"), and cite onemap (Margarido et al. 2007; Taniguti et al. 2023) and R/qtl (Broman et al. 2003).

Licence

MIT. Linkmapper was created by Ebenezer Ogoe, Michael Obeng and Stephen Amoako; the 2026 package was written and is maintained by Ebenezer Ogoe.