get_results {DEP} | R Documentation

## Generate a results table

### Description

`get_results` generates a results table from a proteomics dataset on which differential enrichment analysis was performed.

### Usage

    get_results(dep)

### Arguments

`dep` | SummarizedExperiment, Data object for which differentially enriched proteins are annotated (output from `test_diff()` and `add_rejections()`).

### Value

A data.frame object containing all results variables from the performed analysis.

### Examples

    # 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)

[Package DEP version 1.9.0 Index]