Mismatch between gene expression and features

[TomVuod]

There is a bug in ArrowRead.R file which produces a mismatch between rows in the gene expression matrix and features in rowData.

matchI <- match(i, idxRows, nomatch = 0)
idxI <- which(matchI > 0)
i <- i[idxI]
j <- j[idxI]
i <- matchI[idxI]

The last line replaces the row indices with the corresponding indices of the sorted genes. This behavior has no effect as long as the genes are already sorted, meaning that the idx vector is identical to seq_along(idx). However, if the genes are unsorted, this operation alters the row positions of at least some elements in the assembled matrix, leading to inconsistencies. As a result, the new row indices no longer align with the rows in rowData, which is retrieved independently.
To reproduce this bug it's sufficient to pass to addGeneExpressionMatrix a SummarizedExperiment with genes unsorted relative to their position in the genome. After saving the ArchR project and loading it from the Arrow files the gene expression doesn't match the gene names as rows where
rowData(GeneExpressionMatrix)$idx != seq_along(rowData(GeneExpressionMatrix)$idx).

[immanuelazn]

Hi @TomVuod! Thanks for using ArchR! Please make sure that your post belongs in the Issues section. Only bugs and error reports belong in the Issues section. Usage questions and feature requests should be posted in the Discussions section, not in Issues.

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