get_results {DEP} | R Documentation |
get_results
generates a results table from a proteomics dataset
on which differential enrichment analysis was performed.
get_results(dep)
dep |
SummarizedExperiment,
Data object for which differentially enriched proteins are annotated
(output from |
A data.frame object containing all results variables from the performed analysis.
# Load example data <- UbiLength data <- data[data$Reverse != "+" & data$Potential.contaminant != "+",] data_unique <- make_unique(data, "Gene.names", "Protein.IDs", delim = ";") # Make SummarizedExperiment columns <- grep("LFQ.", colnames(data_unique)) exp_design <- UbiLength_ExpDesign se <- make_se(data_unique, columns, exp_design) # Filter, normalize and impute missing values filt <- filter_missval(se, thr = 0) norm <- normalize_vsn(filt) imputed <- impute(norm, fun = "MinProb", q = 0.01) # Test for differentially expressed proteins diff <- test_diff(imputed, "control", "Ctrl") dep <- add_rejections(diff, alpha = 0.05, lfc = 1) # Get results results <- get_results(dep) colnames(results) significant_proteins <- results[results$significant,] nrow(significant_proteins) head(significant_proteins)