test_gsea: Gene Set Enrichment Analysis

In arnesmits/DEP: Differential Enrichment analysis of Proteomics data

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)

arnesmits/DEP documentation built on Aug. 7, 2019, 10:44 a.m.