MSstatsGroupComparison {MSstats} | R Documentation |
Group comparison
MSstatsGroupComparison( summarized_list, contrast_matrix, save_fitted_models, repeated, samples_info )
summarized_list |
output of MSstatsPrepareForGroupComparison |
contrast_matrix |
contrast matrix |
save_fitted_models |
if TRUE, fitted models will be included in the output |
repeated |
logical, output of checkRepeatedDesign function |
samples_info |
data.table, output of getSamplesInfo function |
QuantData <- dataProcess(SRMRawData, use_log_file = FALSE) group_comparison_input = MSstatsPrepareForGroupComparison(QuantData) levels(QuantData$ProteinLevelData$GROUP) comparison <- matrix(c(-1,0,0,0,0,0,1,0,0,0),nrow=1) row.names(comparison) <- "T7-T1" groups = levels(QuantData$ProteinLevelData$GROUP) colnames(comparison) <- groups[order(as.numeric(groups))] samples_info = getSamplesInfo(QuantData) repeated = checkRepeatedDesign(QuantData) group_comparison = MSstatsGroupComparison(group_comparison_input, comparison, FALSE, repeated, samples_info) length(group_comparison) # list of length equal to number of proteins group_comparison[[1]][[1]] # data used to fit linear model group_comparison[[1]][[2]] # comparison result group_comparison[[2]][[3]] # NULL, because we set save_fitted_models to FALSE