From f8fdf9d21f89784f7dbdd6ce2e3124a857421b5e Mon Sep 17 00:00:00 2001 From: Mateusz Staniak Date: Fri, 17 Mar 2023 14:36:49 +0100 Subject: [PATCH] updated contrast matrix column names check for case when some groups are missing after filtering Abundance=NA --- R/groupComparisonTMT.R | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/R/groupComparisonTMT.R b/R/groupComparisonTMT.R index 0329f8e..eb55b29 100644 --- a/R/groupComparisonTMT.R +++ b/R/groupComparisonTMT.R @@ -71,8 +71,10 @@ groupComparisonTMT = function( summarized = MSstatsPrepareForGroupComparisonTMT(data$ProteinLevelData, remove_norm_channel, remove_empty_channel) - contrast_matrix = MSstats::MSstatsContrastMatrix(contrast.matrix, - unique(summarized$Group)) + conditions = unique(data[["ProteinLevelData"]][["Group"]]) + conditions = setdiff(conditions, c("Empty", "Norm")[c(remove_empty_channel, remove_norm_channel)]) + + contrast_matrix = MSstats::MSstatsContrastMatrix(contrast.matrix, conditions) fitted_models = MSstatsFitComparisonModelsTMT(summarized) FittedModel <- fitted_models$fitted_model names(FittedModel) <- fitted_models$protein