View source: R/groupComparison.R
MSstatsGroupComparisonOutput | 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"]]
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