MSstatsGroupComparisonOutput: Create output of group comparison based on results for...

In MeenaChoi/MSstats: Protein Significance Analysis in DDA, SRM and DIA for Label-free or Label-based Proteomics Experiments

Create output of group comparison based on results for individual proteins

Description

Create output of group comparison based on results for individual proteins

Usage

MSstatsGroupComparisonOutput(input, summarization_output, log_base = 2)

Arguments

input	output of MSstatsGroupComparison function
summarization_output	output of dataProcess function
log_base	base of the logarithm used in fold-change calculation

Value

list, same as the output of 'groupComparison'

Examples

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"]] 
                                                    

MeenaChoi/MSstats documentation built on Nov. 30, 2024, 7:26 a.m.