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Jorisvansteenbrugge
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Mar 6, 2026
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| # CollectFilled functions | |||
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| collapse <- function(column_label, peakgroup_list, index_dup) { | |||
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This function name should be more descriptive collapse_...
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| case_label <- "P" | ||
| control_label <- "C" |
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are these always the same labels? Otherwise it make sense to add them as parameters
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| for (row_index in seq_len(nrow(peakgroup_list))) { | ||
| if (!is.na(peakgroup_list$theormz_HMDB[row_index]) && | ||
| !is.null(peakgroup_list$theormz_HMDB[row_index]) && | ||
| (peakgroup_list$theormz_HMDB[row_index] != "")) { | ||
| peakgroup_list$ppmdev[row_index] <- 10^6 * (as.numeric(as.vector(peakgroup_list$mzmed.pgrp[row_index])) - | ||
| as.numeric(as.vector(peakgroup_list$theormz_HMDB[row_index]))) / | ||
| as.numeric(as.vector(peakgroup_list$theormz_HMDB[row_index])) | ||
| } else { | ||
| peakgroup_list$ppmdev[row_index] <- NA | ||
| } | ||
| } |
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This part is very hard to read. It would benefit from a refactor
| outlist_ident <- outlist_ident[, -which(colnames(outlist_ident) %in% remove_columns)] | ||
| write.table(outlist_ident, file = paste0("outlist_identified_", scanmode, ".txt"), sep = "\t", row.names = FALSE) | ||
| # output in RData format | ||
| # generate output in RData format |
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Suggested change
| # generate output in RData format | |
| # export output in RData format |
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Verschillende functies gemaakt en naar aparte file verplaatst (preprocessing/collect_filled_functions.R).
Unit tests toegevoegd, fixtures/test_peakgroup_list.txt aangepast.
Er stond in de oude versie een filter op geannoteerde piekgroepen met een ppm deviatie groter dan 5; dat is niet meer gewenst. De output van deze stap moet alle piekgroepen bevatten. Het filter is verwijderd.