| 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)