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add initial validation function for spectronaut columns #105

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Merged
tonywu1999 merged 2 commits into from
Mar 20, 2025
Merged

add initial validation function for spectronaut columns #105

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189c353
add initial validation function for spectronaut columns
tonywu1999 Mar 20, 2025
1d0b9c1
add unit tests
tonywu1999 Mar 20, 2025
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17 changes: 17 additions & 0 deletions R/clean_Spectronaut.R
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Original file line number Diff line number Diff line change
Expand Up @@ -7,6 +7,7 @@
FFrgLossType = FExcludedFromQuantification = NULL

spec_input = getInputFile(msstats_object, "input")
.validateSpectronautInput(spec_input)
spec_input = spec_input[FFrgLossType == "noloss", ]

if (is.character(spec_input$FExcludedFromQuantification)) {
Expand All @@ -32,3 +33,19 @@
.logSuccess("Spectronaut", "clean")
spec_input
}

#' Helper method to validate input has necessary columns
#' @param spec_input dataframe input
#' @noRd
.validateSpectronautInput = function(spec_input) {
required_columns = c(
"FFrgLossType", "FExcludedFromQuantification", "PGProteinGroups",
"FGCharge")
missing_columns = setdiff(required_columns, colnames(spec_input))
if (length(missing_columns) > 0) {
msg = paste("The following columns are missing from the input data:",
paste(missing_columns, sep = ", ", collapse = ", "))
getOption("MSstatsLog")("ERROR", msg)
stop(msg)
}
}
41 changes: 40 additions & 1 deletion inst/tinytest/test_converters_SpectronauttoMSstatsFormat.R
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Expand Up @@ -15,4 +15,43 @@ expect_true("ProductCharge" %in% colnames(output))
expect_true("IsotopeLabelType" %in% colnames(output))
expect_true("Condition" %in% colnames(output))
expect_true("BioReplicate" %in% colnames(output))
expect_true("Fraction" %in% colnames(output))
expect_true("Fraction" %in% colnames(output))


# Test SpectronauttoMSstatsFormat Missing Columns ---------------------------
spectronaut_raw = system.file("tinytest/raw_data/Spectronaut/spectronaut_input.csv",
package = "MSstatsConvert")
spectronaut_raw = data.table::fread(spectronaut_raw)
spectronaut_raw$F.ExcludedFromQuantification = NULL
expect_error(
SpectronauttoMSstatsFormat(spectronaut_raw, use_log_file = FALSE),
"The following columns are missing from the input data: FExcludedFromQuantification"
)

spectronaut_raw = system.file("tinytest/raw_data/Spectronaut/spectronaut_input.csv",
package = "MSstatsConvert")
spectronaut_raw = data.table::fread(spectronaut_raw)
spectronaut_raw$F.FrgLossType = NULL
expect_error(
SpectronauttoMSstatsFormat(spectronaut_raw, use_log_file = FALSE),
"The following columns are missing from the input data: FFrgLossType"
)

spectronaut_raw = system.file("tinytest/raw_data/Spectronaut/spectronaut_input.csv",
package = "MSstatsConvert")
spectronaut_raw = data.table::fread(spectronaut_raw)
spectronaut_raw$PG.ProteinGroups = NULL
expect_error(
SpectronauttoMSstatsFormat(spectronaut_raw, use_log_file = FALSE),
"The following columns are missing from the input data: PGProteinGroups"
)

spectronaut_raw = system.file("tinytest/raw_data/Spectronaut/spectronaut_input.csv",
package = "MSstatsConvert")
spectronaut_raw = data.table::fread(spectronaut_raw)
spectronaut_raw$FG.Charge = NULL
expect_error(
SpectronauttoMSstatsFormat(spectronaut_raw, use_log_file = FALSE),
"The following columns are missing from the input data: FGCharge"
)

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