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Add hotfix DIMS/v3.3.1 to main
Jorisvansteenbrugge
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Mar 6, 2026
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| trim_left_pos <- round(pos_times[length(pos_times) * (trim * 1.5)]) | ||
| trim_right_pos <- round(pos_times[length(pos_times) * (1 - (trim * 0.5))]) |
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I am a bit confused what trim is exactly?
Why is trim a parameter, but the 1.5 and 0.5 are hard coded. I would make all of them function parameters (with a default value)
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| #' @param scantimes: vector of scan times in seconds | ||
| #' @param polarities: vector of polarities (positive or negative) |
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I am missing a description of the trim param
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| # trim (remove) scans at the start and end (10%) for negative | ||
| trim_left_neg <- round(neg_times[length(neg_times) * trim]) | ||
| trim_right_neg <- round(neg_times[length(neg_times) * (1 - trim)]) |
| #' @param mzrange: vector of minimum and maximum m/z values (integeers) | ||
| #' @param resol: value for resolution (integer) | ||
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| # initialize |
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| # initialize |
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in get_breaks_for_bins() you have as a comment fwhm (width of peaks) is assumed to be constant within a segment.
Would it make sense to add a test to see what happens if that is not the case?
| script: | ||
| """ | ||
| Rscript ${baseDir}/CustomModules/DIMS/GenerateBreaks.R $mzML_file ./ $params.trim $params.resolution | ||
| Rscript ${baseDir}/CustomModules/DIMS/GenerateBreaks.R $mzML_file $params.trim $params.resolution |
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Please refrain from referencing params and baseDir in the script block.
See #94 (comment) and #94 (comment)
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Code refactored, moved into functions. Output for trim_parameters and breaks separated. This has implications for other steps in the pipeline, but this has already been set up in refactor_PeakFinding (which is not in develop yet).
Unit tests added.