MSstatsGroupComparisonOutput {MSstats} | R Documentation |
Create output of group comparison based on results for individual proteins
MSstatsGroupComparisonOutput(input, summarization_output, log_base = 2)
input |
output of MSstatsGroupComparison function |
summarization_output |
output of dataProcess function |
log_base |
base of the logarithm used in fold-change calculation |
list, same as the output of 'groupComparison'
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) group_comparison_final = MSstatsGroupComparisonOutput(group_comparison, QuantData) group_comparison_final[["ComparisonResult"]]