run_test: Run enrichment analysis procedure

In koralgooll/MulEA: MulEA - A Tool for Multi Enrichment Analysis

Run enrichment analysis procedure

Description

This is a generic function that chooses an enrichment analysis procedure based on the model class and runs the analysis.

Usage

run_test(model)

Arguments

model

An S4 object which represents one of Mulea's Tests. See details for more information.

Details

The function requires the definition of a model. Models currently implemented in MulEA include Gene Set Enrichment Analysis (GSEA) and Over-Representation Analysis (ORA). These models must be defined through their specific functions which are provided in this package.

Value

Results in form of data frame. Structure of data frame depends on object processed by this generic method.

See Also

gsea, ora

Examples

modelDfFromFile <- read_gmt(
  file = system.file(package="MulEA", "extdata", "model.gmt"))
dataFromExperiment <- c(
  "FBgn0004407", "FBgn0010438", "FBgn0003742", "FBgn0029709", "FBgn0030341",
  "FBgn0037044", "FBgn0002887", "FBgn0028434", "FBgn0030170", "FBgn0263831")
dataFromExperimentPool <- unique(
  c(c("FBgn0033690", "FBgn0261618", "FBgn0004407", "FBgn0010438",
      "FBgn0032154", "FBgn0039930", "FBgn0040268", "FBgn0013674",
      "FBgn0037008", "FBgn0003116", "FBgn0037743", "FBgn0035401",
      "FBgn0037044", "FBgn0051005", "FBgn0026737", "FBgn0026751",
      "FBgn0038704", "FBgn0002887", "FBgn0028434", "FBgn0030170",
      "FBgn0263831", "FBgn0000579"),
   c("FBgn0066666", "FBgn0000000", "FBgn0099999", "FBgn0011111",
     "FBgn0022222", "FBgn0777777", "FBgn0333333", "FBgn0003742",
     "FBgn0029709", "FBgn0030341")))
setBasedTest <- ora(gmt = modelDfFromFile, element_names = dataFromExperiment,
                   number_of_cpu_threads = 2)
setBasedTestWithPool <- ora(gmt = modelDfFromFile,
                            element_names = dataFromExperiment,
                            background_element_names = dataFromExperimentPool,
                            number_of_cpu_threads = 2)
setBasedTestWithPoolAndAdjust <- ora(gmt = modelDfFromFile,
                                     element_names = dataFromExperiment,
                                     background_element_names = dataFromExperimentPool,
                                     p_value_adjustment_method = "BH",
                                     number_of_cpu_threads = 2)
setBasedTestRes <- run_test(setBasedTest)
setBasedTestWithPoolRes <- run_test(setBasedTestWithPool)
setBasedTestWithPoolAndAdjustRes <- run_test(setBasedTestWithPoolAndAdjust)
dataFromExperimentScores <- c(0.09, 0.11, 0.15, 0.20, 0.21, 0.24, 0.28,
                              0.30, 0.45, 0.50)
GSEASubramanian <- gsea(
  method = "Subramanian",
  gmt = modelDfFromFile,
  element_names = dataFromExperiment,
  element_scores = dataFromExperimentScores)
GSEASubramanianRes <- MulEA::run_test(GSEASubramanian)

koralgooll/MulEA documentation built on Nov. 23, 2023, 3:27 p.m.