`fastreseg_full_pipeline()` does not account for counts matrices with clashing probe order

[istvankleijn]

In the fastreseg_full_pipeline(), I am running into problems when the updated_perCellExprs matrices do not have the probes in a consistent order across all FOVs. The final merge step in the pipeline then silently mixes up the probes because cbind assumes that all columns are in the same order.

FastReseg/R/fastReseg_full_pipeline.R

Line 485 in efad6dc

updated_perCellExprs <- do.call(cbind, updated_perCellExprs)

This lead to some strange downstream results which disappeared when I merged the per-FOV matrices from the each_segRes.rds files manually and ensured that all columns and rows matched up.

I think this may have something to do with (control) probes that remain undetected being pushed to the end of the list but I am not sure about this.

[github-actions]

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[lidanwu]

@istvankleijn Thanks for the info. The order of probes are managed by some supporting function else where. But you're right that it would be cleaner to match up the rows when combine them together. I'll update the package with a fix. Thank you!

[lidanwu]

The PR #56 addresses the probe alignment upon combination for package version v1.0.4 and above.