MSstatsGroupComparisonSingleProtein: Group comparison for a single protein

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

Group comparison for a single protein

Description

Group comparison for a single protein

Usage

MSstatsGroupComparisonSingleProtein(
  single_protein,
  contrast_matrix,
  repeated,
  groups,
  samples_info,
  save_fitted_models,
  has_imputed
)

Arguments

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

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)
single_output <- MSstatsGroupComparisonSingleProtein(
  group_comparison_input[[1]], comparison, repeated, groups, samples_info,
  FALSE, TRUE)
single_output # same as a single element of MSstatsGroupComparison output

MeenaChoi/MSstats documentation built on Nov. 10, 2024, 2:43 p.m.