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addGeneScoreMatrix: GeneScoreMatrix is silently all-NaN when gene widths are equal (divide by max(m)-min(m) = 0) #2334
Description
In .addGeneScoreMat (default useTSS = FALSE, gene-body path), R/MatrixGeneScores.R at v1.0.3:
270 m <- 1 / width(geneRegions)
271 geneRegions$geneWeight <- 1 + m * (geneScaleFactor - 1) / (max(m) - min(m))If every gene region has the same width, max(m) - min(m) is 0, every geneWeight is Inf/NaN, and the whole GeneScoreMatrix comes out NaN, with no error or warning. The failure only shows up later, far from its cause: getMarkerFeatures(useMatrix = "GeneScoreMatrix") stops with missing value where TRUE/FALSE needed.
This bit us on a small synthetic genome with uniform gene lengths (ArchR 1.0.3 from bioconda r-archr, R 4.4, on linux-aarch64 and linux-64 alike). Varying the gene lengths makes the matrix finite.
A second, possibly related question: the expression is not a min-max scaling of m. That would be 1 + (m - min(m)) * (geneScaleFactor - 1) / (max(m) - min(m)), mapping to [1, geneScaleFactor]. As written, the weights span [1 + min(m)·k, 1 + max(m)·k], which reaches geneScaleFactor only when min(m) is close to 0. If min-max is the intent, the fix covers both issues. If it isn't, a guard is enough, e.g.
rng <- max(m) - min(m)
geneRegions$geneWeight <- if (rng > 0) 1 + m * (geneScaleFactor - 1) / rng else geneScaleFactorEither way, it would help to error (or warn) on a non-finite GeneScoreMatrix at creation time rather than at getMarkerFeatures.
Activity
immanuelazn commentedon Oct 16, 2026
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