NEWS

linkmapper 0.2.0

A rewrite of the app as a modular package.

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.

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.

run_linkmapper(), validate_lm_file() and group_markers() keep their 0.1 behaviour.