analyze_dep {DEP} | R Documentation

## Differential expression analysis

### Description

`analyze_dep` tests for differential expression of proteins based on protein-wise linear models and empirical Bayes statistics using limma.

### Usage

    analyze_dep(se, type = c("all", "control", "manual"), control = NULL,
      alpha = 0.05, lfc = 1, test = NULL, design_formula = formula(~0 +
      condition))

### Arguments

`se` | SummarizedExperiment, Proteomics data with unique names and identifiers annotated in 'name' and 'ID' columns. Additionally, the colData should contain sample annotation including 'label', 'condition' and 'replicate' columns. The appropriate columns and objects can be generated using `make_se` or `make_se_parse`.
`type` | "all", "control" or "manual", The type of contrasts that will be tested. This can be all possible pairwise comparisons ("all"), limited to the comparisons versus the control ("control"), or manually defined contrasts ("manual").
`control` | Character(1), The condition to which contrasts are generated (a control condition would be most appropriate).
`alpha` | Numeric(1), Sets the threshold for the adjusted P value.
`lfc` | Numeric(1), Sets the threshold for the log2 fold change.
`test` | Character, The contrasts that will be tested if type = "manual". These should be formatted as "SampleA_vs_SampleB" or c("SampleA_vs_SampleC", "SampleB_vs_SampleC").
`design_formula` | Formula, Used to create the design matrix.

### Value

A SummarizedExperiment object containing FDR estimates of differential expression and logical columns indicating significant proteins.

### Examples

    # Load datasets
    data <- UbiLength
    exp_design <- UbiLength_ExpDesign

    # Import and process data
    se <- import_MaxQuant(data, exp_design)
    processed <- process(se)

    # Differential protein expression analysis
    dep <- analyze_dep(processed, "control", "Ctrl")
    dep <- analyze_dep(processed, "control", "Ctrl",
        alpha = 0.01, lfc = log2(1.5))
    dep <- analyze_dep(processed, "manual", test = c("Ubi6_vs_Ubi4"))

[Package DEP version 1.9.0 Index]