test_gsea {DEP} | R Documentation |
test_gsea
tests for enriched gene sets
in the differentially enriched proteins.
This can be done independently for the different contrasts.
test_gsea(dep, databases = c("GO_Molecular_Function_2017b", "GO_Cellular_Component_2017b", "GO_Biological_Process_2017b"), contrasts = TRUE)
dep |
SummarizedExperiment,
Data object for which differentially enriched proteins are annotated
(output from |
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. |
A data.frame with enrichment terms (generated by enrichr
)
# 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)