topFeatures {msqrob2} | R Documentation |
Summary table of the differentially expressed Features
topFeatures(models, contrast, adjust.method = "BH", sort = TRUE, alpha = 1)
models |
A list with elements of the class |
contrast |
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adjust.method |
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sort |
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alpha |
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A dataframe with log2 fold changes (logFC), standard errors (se), degrees of freedom of the test (df), t-test statistic (t), p-values (pval) and adjusted pvalues (adjPval) using the specified adjust.method in the p.adjust function of the stats package.
Lieven Clement
data(pe) # Aggregate peptide intensities in protein expression values pe <- aggregateFeatures(pe, i = "peptide", fcol = "Proteins", name = "protein") # Fit msqrob model pe <- msqrob(pe, i = "protein", formula = ~condition) # Define contrast getCoef(rowData(pe[["protein"]])$msqrobModels[[1]]) # Assess log2 fold change between condition c and condition b: L <- makeContrast("conditionc - conditionb=0", c("conditionb", "conditionc")) topDeProteins <- topFeatures(rowData(pe[["protein"]])$msqrobModels, L)