get_df_long {DEP} | R Documentation |
get_df_long
generate a wide data.frame from a SummarizedExperiment.
get_df_long(se)
se |
SummarizedExperiment,
Proteomics data (output from |
A data.frame object containing all data in a wide format, where each row represents a single measurement.
# 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 a long data.frame long <- get_df_long(dep) colnames(long)