MSstatsGroupComparisonSingleProtein {MSstats} | R Documentation |
Group comparison for a single protein
MSstatsGroupComparisonSingleProtein( single_protein, contrast_matrix, repeated, groups, samples_info, save_fitted_models, has_imputed )
single_protein |
data.table with summarized data for a single protein |
contrast_matrix |
contrast matrix |
repeated |
if TRUE, repeated measurements will be modeled |
groups |
unique labels of experimental conditions |
samples_info |
number of runs per group |
save_fitted_models |
if TRUE, fitted model will be saved. If not, it will be replaced with NULL |
has_imputed |
TRUE if missing values have been imputed |
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) single_output <- MSstatsGroupComparisonSingleProtein( group_comparison_input[[1]], comparison, repeated, groups, samples_info, FALSE, TRUE) single_output # same as a single element of MSstatsGroupComparison output