test_gsea {DEP} | R Documentation

## Gene Set Enrichment Analysis

### Description

`test_gsea` tests for enriched gene sets in the differentially enriched proteins. This can be done independently for the different contrasts.

### Usage

    test_gsea(dep, databases = c("GO_Molecular_Function_2017b",
      "GO_Cellular_Component_2017b", "GO_Biological_Process_2017b"),
      contrasts = TRUE)

### Arguments

`dep` | SummarizedExperiment, Data object for which differentially enriched proteins are annotated (output from `test_diff()` and `add_rejections()`).
`databases` | Character, Databases to search for gene set enrichment. See http://amp.pharm.mssm.edu/Enrichr/ for available databases.
`contrasts` | Logical(1), Whether or not to perform the gene set enrichment analysis independently for the different contrasts.

### Value

A data.frame with enrichment terms (generated by `enrichr`)

### 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 <- diff <- test_diff(imputed, "control", "Ctrl")
    dep <- add_rejections(diff, alpha = 0.05, lfc = 1)

    ## Not run:

    # Test enrichments
    gsea_results_per_contrast <- test_gsea(dep)
    gsea_results <- test_gsea(dep, contrasts = FALSE)

    gsea_kegg <- test_gsea(dep, databases = "KEGG_2016")

    ## End(Not run)

[Package DEP version 1.12.0 Index]