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Addresses #106 |
gpatoine
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Nov 5, 2025
| # Merge assay, sample, ms_run, and study_variable metadata | ||
| if ("sample_ref" %in% names(assay_tab)) assay_tab$sample_id <- assay_tab$sample_ref | ||
| if ("ms_run_ref" %in% names(assay_tab)) assay_tab$ms_run_id <- assay_tab$ms_run_ref | ||
| if (!is.null(sample_tab) && "sample_id" %in% names(assay_tab)) |
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Here and below: Please add curly brackets for if-statement contents on a different line.
gpatoine
reviewed
Nov 5, 2025
| # Build SummarizedExperiment for a section | ||
| build_se <- function(tab, id_col, cd) { | ||
| qcols <- get_assay_quant_cols(tab) | ||
| if (!length(qcols)) stop("No abundance_assay[...] columns in ", id_col, " section.") |
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Same with curly brackets here.
gpatoine
reviewed
Nov 5, 2025
| } | ||
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| # Cast regular fields to wide | ||
| regular_wide <- reshape(regular_df, idvar = idvar, timevar = field_col, v.names = value_col, direction = "wide") |
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Getting a warning: "some constant variables (field) are really varying". Is that an issue?
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Implements readMzTabM() function to import mzTab-M files and convert them to QFeatures objects.
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