View source: R/groupComparison.R
MSstatsGroupComparisonSingleProtein | 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
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