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mmconvert

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R package mmconvert by rqtl — release notes from GitHub.

github.com/rqtl/mmconvert ↗

A single-purpose mouse map interpolator that solved its problem in 2023 and has coasted since

r-packagegeneticsgenome-buildreference-datacran-maintenance
◆Current state
mmconvert does one thing: interpolate between GRCm39 physical positions and the revised Cox genetic map for mouse MUGA array markers. The substantive work all landed in a burst across 2021-2023 — the initial function, the GRCm39 annotation dataset, cross2_to_grcm39(), the recomputed Cox maps and their smoothed replacement. Everything since is upkeep: a warning-message fix in 0.12, and 0.14 is a test adjustment to silence a CRAN Note with no code change at all.
◆Where it's heading
The package has reached the natural end state of a reference-data converter — the reference data stopped moving, so the package stopped moving. Releases now arrive roughly annually and exist to keep CRAN checks green. The 0.14 release shipped the same day as sibling qtl2convert 0.36, confirming these are batch maintenance passes across the maintainer's packages rather than independent development.
◆Prediction
Without a new mouse genome build or a revised Cox map, the next release is likely another CRAN-check accommodation rather than new functionality.

◆Recent moves

  1. 1mo ago

    Test adjustment to clear a CRAN Note

    A release containing only a test tweak to avoid a CRAN Note — no code, data, or interface change. It shipped the same day as qtl2convert 0.36, marking it as part of a batch maintenance pass across the maintainer's packages.

    View source ↗
  2. 1y ago

    Fixes a malformed warning message in mmconvert()

    A one-line correction to a warning message. The two-year gap on either side of it shows how settled the package's actual functionality is.

    View source ↗
  3. 3y ago

    Omits X chromosome positions for sex-averaged and male maps

    Suppresses X chromosome output when input_type is ave_cM or male_cM, where those positions aren't meaningful. A small correctness refinement to the interpolation surface established earlier that year.

    View source ↗
  4. 3y ago

    CRAN release adds chromosome lengths and smoothed Cox maps

    The CRAN debut, bundling the grcm39_chrlen dataset, out-of-range position warnings, a marker-count threshold for array guessing, and a smoothed replacement for the Cox map that permits recombination in previously zero-recombination intervals. This is the release that made the package broadly usable.

    View source ↗
  5. 3y ago

    Recomputed Cox genetic maps and combined-array support

    Re-estimates the Cox genetic maps with the original crimap software and revises MUGAmaps to match, while teaching cross2_to_grcm39() to handle markers spanning GigaMUGA and MegaMUGA. Underlying reference data changing beneath a converter is the highest-impact change this package can make.

    View source ↗
  6. 4y ago

    Repoints data sources from master to main branches

    Updates the MUGAarrays and qtl2data branch references from master to main. Pure plumbing, with no effect on interpolation results.

    View source ↗