diff --git a/R/converters_DIANNtoMSstatsFormat.R b/R/converters_DIANNtoMSstatsFormat.R index 82268c8a..78135f6a 100644 --- a/R/converters_DIANNtoMSstatsFormat.R +++ b/R/converters_DIANNtoMSstatsFormat.R @@ -86,7 +86,6 @@ DIANNtoMSstatsFormat = function( input = MSstatsConvert::MSstatsImport(list(input = input), "MSstats", "DIANN") - # browser() input = MSstatsConvert::MSstatsClean( input, MBR = MBR, quantificationColumn = quantificationColumn, calculateAnomalyScores = calculateAnomalyScores, @@ -105,7 +104,6 @@ DIANNtoMSstatsFormat = function( msg = paste0('** Filtering on Global Q Value < ', global_qvalue_cutoff) getOption("MSstatsLog")("INFO", msg) getOption("MSstatsMsg")("INFO", msg) - # browser() input[DetectionQValue >= global_qvalue_cutoff, Intensity := 0] if (MBR) { @@ -138,7 +136,6 @@ DIANNtoMSstatsFormat = function( feature_columns = c("PeptideSequence", "PrecursorCharge", "FragmentIon", "ProductCharge") - # browser() input = MSstatsConvert::MSstatsPreprocess( input, annotation, @@ -156,21 +153,18 @@ DIANNtoMSstatsFormat = function( IsotopeLabelType = "Light"), anomaly_metrics = anomalyModelFeatures) input[, Intensity := ifelse(Intensity == 0, NA, Intensity)] - # browser() input = MSstatsConvert::MSstatsBalancedDesign(input, feature_columns, fill_incomplete = TRUE, handle_fractions = FALSE, remove_few = removeFewMeasurements, anomaly_metrics = anomalyModelFeatures ) - # browser() if (calculateAnomalyScores){ input = MSstatsConvert::MSstatsAnomalyScores( input, anomalyModelFeatures, anomalyModelFeatureTemporal, removeMissingFeatures, anomalyModelFeatureCount, runOrder, n_trees, max_depth, numberOfCores) } - # browser() msg_final = paste("** Finished preprocessing. The dataset is ready", "to be processed by the dataProcess function.") getOption("MSstatsLog")("INFO", msg_final)