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fix(spectronaut): Enable Fraction column to be processed #137

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Merged
tonywu1999 merged 3 commits into from
Jun 2, 2026
Merged

fix(spectronaut): Enable Fraction column to be processed #137

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846c142
fix(spectronaut): Enable Fraction column to be processed
tonywu1999 Jun 2, 2026
c28893d
fix edge case of NA in R.Fraction
tonywu1999 Jun 2, 2026
bca444c
add warning
tonywu1999 Jun 2, 2026
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23 changes: 18 additions & 5 deletions R/clean_Spectronaut.R
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Original file line number Diff line number Diff line change
Expand Up @@ -8,7 +8,7 @@
anomalyModelFeatures,
peptideSequenceColumn = "EG.ModifiedSequence",
heavyLabels = NULL) {
FFrgLossType = FExcludedFromQuantification = NULL
FFrgLossType = FExcludedFromQuantification = Fraction = NULL

spec_input = getInputFile(msstats_object, "input")
.validateSpectronautInput(spec_input, peptideSequenceColumn)
Expand All @@ -29,8 +29,8 @@

cols = c(protein_col, peptide_col, "FGCharge", "FFrgIon",
f_charge_col, "RFileName", "RCondition", "RReplicate",
"EGQvalue", pg_qval_col, interference_col, exclude_col,
intensity_col)
"RFraction", "EGQvalue", pg_qval_col, interference_col,
exclude_col, intensity_col)
if (calculateAnomalyScores){
cols = c(cols, anomalyModelFeatures)
}
Expand All @@ -41,11 +41,24 @@
spec_input,
c(protein_col, peptide_col, "FGCharge", "FFrgIon",
f_charge_col, "RFileName", intensity_col,
"RCondition", "RReplicate"),
"RCondition", "RReplicate", "RFraction"),
c("ProteinName", "PeptideSequence", "PrecursorCharge", "FragmentIon",
"ProductCharge", "Run", "Intensity", "Condition", "BioReplicate"),
"ProductCharge", "Run", "Intensity", "Condition", "BioReplicate",
"Fraction"),
skip_absent = TRUE)

if ("Fraction" %in% colnames(spec_input)) {
n_missing_fraction = sum(is.na(spec_input$Fraction))
if (n_missing_fraction > 0) {
msg = paste("**", n_missing_fraction,
"row(s) have missing (NA) values in the Fraction column.",
"These will be assigned to Fraction 1.")
getOption("MSstatsLog")("WARN", msg)
getOption("MSstatsMsg")("WARN", msg)
spec_input[is.na(Fraction), Fraction := 1]
}
}

spec_input = .assignSpectronautIsotopeLabelType(
spec_input, heavyLabels)

Expand Down
23 changes: 23 additions & 0 deletions inst/tinytest/test_clean_Spectronaut.R
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Original file line number Diff line number Diff line change
Expand Up @@ -9,6 +9,29 @@ output = MSstatsConvert:::.cleanRawSpectronaut(msstats_input, intensity = 'FG.MS
calculateAnomalyScores = FALSE,
anomalyModelFeatures = c())
expect_true(all(output$Intensity == 100000))
expect_false("Fraction" %in% colnames(output))

spectronaut_frac = data.table::copy(spectronaut_raw)
spectronaut_frac$R.Fraction = 2L
msstats_frac = MSstatsConvert::MSstatsImport(
list(input = spectronaut_frac), "MSstats", "Spectronaut")
output_frac = MSstatsConvert:::.cleanRawSpectronaut(msstats_frac, intensity = 'FG.MS1Quantity',
calculateAnomalyScores = FALSE,
anomalyModelFeatures = c())
expect_true("Fraction" %in% colnames(output_frac))
expect_false("RFraction" %in% colnames(output_frac))
expect_true(all(output_frac$Fraction == 2L))

spectronaut_frac_na = data.table::copy(spectronaut_raw)
spectronaut_frac_na$R.Fraction = NA_integer_
msstats_frac_na = MSstatsConvert::MSstatsImport(
list(input = spectronaut_frac_na), "MSstats", "Spectronaut")
output_frac_na = MSstatsConvert:::.cleanRawSpectronaut(msstats_frac_na, intensity = 'FG.MS1Quantity',
calculateAnomalyScores = FALSE,
anomalyModelFeatures = c())
expect_true("Fraction" %in% colnames(output_frac_na))
expect_false(any(is.na(output_frac_na$Fraction)))
expect_true(all(output_frac_na$Fraction == 1))

expect_error(MSstatsConvert:::.cleanRawSpectronaut(msstats_input, intensity = 'invalid',
calculateAnomalyScores = FALSE,
Expand Down
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