ora-class: An S4 class to represent a set based tests in Mulea.
In koralgooll/MulEA: MulEA - A Tool for Multi Enrichment Analysis

ora-class

R Documentation

An S4 class to represent a set based tests in Mulea.

Description

An S4 class to represent a set based tests in Mulea.

Usage

## S4 method for signature 'ora'
run_test(model)

Arguments

model

Object of s4 class represents Mulea Test.

Value

ora object. This object represents set based tests.

run_test method for ora object. Returns results of counting using methods from set based area.

Methods (by generic)

run_test(ora): runs test calculations.

Slots

method: A method from set based methods to count results. Possible values: "Hypergeometric", "SetBasedEnrichment".
gmt: A data.frame representing GMT's reprezentation of model.
element_names: A data from experiment to analize accross model.
background_element_names: A background data to count test.
p_value_adjustment_method: A type of algorithm used to adjust values. Possible values: "eFDR" and all from p.adjust stats documentation.
number_of_permutations: A number of permutations used in set based enrichment test. Default value is 10000.
number_of_cpu_threads: Number of processor threads used in calculations.

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
 )
setBaseTestWithPermutationTestAdjustment <- ora(
  gmt = modelDfFromFile,
  element_names = dataFromExperiment,
  p_value_adjustment_method = "eFDR",
  number_of_cpu_threads = 2
 )
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
)
setBaseTestWithPermutationTestAdjustment <- ora(
  gmt = modelDfFromFile,
  element_names = dataFromExperiment,
  p_value_adjustment_method = "eFDR",
  number_of_cpu_threads = 2
)
setBasedTestRes <- run_test(setBasedTest)
setBasedTestWithPoolRes <- run_test(setBasedTestWithPool)
setBasedTestWithPoolAndAdjustRes <- run_test(setBasedTestWithPoolAndAdjust)
setBaseTestWithPermutationTestAdjustmentRes <- run_test(setBaseTestWithPermutationTestAdjustment)

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