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Fix turnover #124

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Merged
tonywu1999 merged 2 commits into from
Apr 7, 2026
Merged

Fix turnover #124

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03ab8eb
fix turnover code
tonywu1999 Apr 7, 2026
bacc483
add unit tests verifying intensities preserved, number of rows are co…
tonywu1999 Apr 7, 2026
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9 changes: 5 additions & 4 deletions R/converters_SpectronauttoMSstatsFormat.R
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Original file line number Diff line number Diff line change
Expand Up @@ -139,14 +139,15 @@ SpectronauttoMSstatsFormat = function(

feature_columns = c("PeptideSequence", "PrecursorCharge",
"FragmentIon", "ProductCharge")

fill_isotope_label_type = if (is.null(heavyLabels))
list("IsotopeLabelType" = "L") else list()
preprocess_feature_columns = if ("IsotopeLabelType" %in% colnames(input))
c(feature_columns, "IsotopeLabelType") else feature_columns
fill_isotope_label_type = if ("IsotopeLabelType" %in% colnames(input))
list() else list("IsotopeLabelType" = "L")

input = MSstatsConvert::MSstatsPreprocess(
input,
annotation,
feature_columns,
preprocess_feature_columns,
remove_shared_peptides = useUniquePeptide,
remove_single_feature_proteins = removeProtein_with1Feature,
feature_cleaning = list(remove_features_with_few_measurements = removeFewMeasurements,
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14 changes: 14 additions & 0 deletions inst/tinytest/test_converters_SpectronauttoMSstatsFormat.R
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Expand Up @@ -427,3 +427,17 @@ output_leu = SpectronauttoMSstatsFormat(
use_log_file = FALSE
)
expect_false("H" %in% unique(output_leu$IsotopeLabelType))

# Verify intensity values for ANGYTTEYSASVK are preserved from FG.MS1Quantity
output_heavy = data.table::as.data.table(output_heavy)
angyt_input_intensities = sort(
boxcar_raw[PEP.StrippedSequence == "ANGYTTEYSASVK", FG.MS1Quantity])
angyt_output_intensities = sort(
output_heavy[grepl("ANGYTTEYSASVK", PeptideSequence, fixed = TRUE), Intensity])
expect_equivalent(angyt_input_intensities, angyt_output_intensities)

# Verify row count for ANGYTTEYSASVK is 2 * number of bioreplicates
# (one row per bioreplicate for heavy label, one for light label)
n_bioreplicates = length(unique(boxcar_raw$R.Replicate))
angyt_rows = subset(output_heavy, grepl("ANGYTTEYSASVK", PeptideSequence, fixed = TRUE))
expect_equal(nrow(angyt_rows), 2L * n_bioreplicates)
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