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Changelog

Source: NEWS.md

linkmapper 0.2.0

A rewrite of the app as a modular package.

New

  • Backcross and recombinant inbred line populations, alongside F2 intercrosses; onemap raw files as well as MAPMAKER.
  • Trait files in CSV, in addition to traits in the genotype file.
  • Segregation tests with Bonferroni correction, missing-data summaries and marker filters.
  • Seriation ordering, Haldane distances, and recombination-fraction heatmaps per linkage group.
  • Interactive linkage map with QTL support intervals; MapChart, CSV and Excel exports.
  • QTL mapping with R/qtl: Haley-Knott, EM or imputation interval mapping and composite interval mapping, permutation thresholds, 1.5-LOD support intervals, variance explained, effects and genotype plots.
  • HTML report, reproducible R script and session files; PNG, SVG and PDF for every figure.
  • Horizontal step bar, guided tour, dark mode and its own visual identity.
  • read_cross(), qc_summary(), filter_markers(), linkage_groups(), order_groups(), build_cross(), scan_qtl(), run_analysis() and related functions are exported.

Fixed

  • Analysis state was held in global variables, so sessions on the hosted app could interfere with each other.
  • The QTL step did not detect QTL on the demo data.
  • The map image was written to the working directory.
  • Marker ordering was not reproducible between runs.

Compatibility