add_rejections {DEP} | R Documentation |
add_rejections
marks significant proteins based on defined cutoffs.
add_rejections(diff, alpha = 0.05, lfc = 1)
diff |
SummarizedExperiment,
Proteomics dataset on which differential enrichment analysis
has been performed (output from |
alpha |
Numeric(1), Sets the threshold for the adjusted P value. |
lfc |
Numeric(1), Sets the threshold for the log2 fold change. |
A SummarizedExperiment object annotated with logical columns indicating significant proteins.
# 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)