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BasMonkey
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Jan 19, 2026
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I've made some remarks about performance and code duplication. Please see the comments left on the code.
DIMS/GenerateQCOutput.R
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| is_selected <- is_pos_selection_subset$HMDB_name[line_index] | ||
| thresh_selected <- all_is_thresholds$plasma$pos[which(all_is_thresholds$names$pos == is_selected)] | ||
| if (is_pos_selection_subset$Intensity[line_index] < thresh_selected) { | ||
| is_below_threshold <- rbind(is_below_threshold, is_pos_selection_subset[line_index, ]) |
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Avoid rbind() in a loop, since it repeatedly reallocates and copies the data frame, which is inefficient and may use a huge amount of ram for larger datasets. Consider collecting indices or rows first and binding once at the end.
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Duly noted. This is a very small data frame, so I'll leave it as is, but in the refactor for v3.5 where all scripts are evaluated, I will take this point into consideration.
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Feb 20, 2026
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Deze feature zorgt ervoor dat er extra QC informatie vanuit de DIMS pipeline in de eindmail komt, zodat de gebruiker in 1 oogopslag de kwaliteit van de run kan beoordelen.
Verschillende stappen van de pipeline, met name AverageTechReplicates en GenerateQCOutput, genereren extra txt bestanden, die als content opgenomen worden in DIMS.nf.