readQFeatures(): don't ignore colData$quantCols#234
Merged
cvanderaa merged 6 commits intorformassspectrometry:masterfrom Oct 21, 2025
Merged
readQFeatures(): don't ignore colData$quantCols#234cvanderaa merged 6 commits intorformassspectrometry:masterfrom
cvanderaa merged 6 commits intorformassspectrometry:masterfrom
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Member
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Hi Alexey, thank you for your PR. Could you provide a simple example that shows the issue and then make use of it in a unit test? I am happy to write the unit test myself if you aren't familiar with |
Author
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@lgatto I've added 2 unit tests with shuffled colData that fail without the fix. |
Member
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Thank yo @alyst - we will review the PR before merging. |
cvanderaa
reviewed
May 28, 2025
added 4 commits
June 21, 2025 15:29
remove quantCols argument since it is not used, and the rownames should be derived from colData$quantCols and colData$runCol
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Author
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@cvanderaa @lgatto Could you please take a look at the PR -- I have tried to address your code review comments? Thank you! |
Member
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Sorry for the delay. @cvanderaa - could you check and merge, please. |
Member
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(FYI @alyst, Chris is on holidays until next week) |
lgatto
approved these changes
Oct 21, 2025
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I think the current version has a bug that, if there are no run information, the row names of
colDataare unconditionally assigned to thesampleNames(the column names of the data).But the order of rows in colData might be different from
sampleNames.The correct behaviour should be to respect the
quantColsas they are provided by the user (matchingquantColstosampleNamesand reordering of colData rows happens later).The current behaviour leads to errors in the downstream analysis (e.g. msqrob2), since matching data columns to the experimental design information is incorrect.