tests/testthat/to_review/test-association_analysis.R
In drake69/semseeker: Stochastic Epigenetic Mutations SEM Seeker
test_that("association_analysis", {
####################################################################################
semseeker( sample_sheet = mySampleSheet,methylation_data = methylation_data,result_folder = tempFolder,parallel_strategy=parallel_strategy, figures="BOTH",
markers=c("BETA"), areas=c("PROBE","CHR","GENE"))
####################################################################################
inferenceFolder <- file.path(tempFolder,"Inference")
inference_details <- expand.grid("independent_variable"= "Phenotest",
"covariates"=c("Covariates1+Covariates2"),
"family_test"=c("gaussian"),
"transformation"="",
"depth_analysis"=3,
"filter_p_value" = FALSE)
association_analysis(inference_details = inference_details, result_folder = tempFolder, parallel_strategy=parallel_strategy,figures="BOTH",
markers=c("DELTAS","DELTAQ","BETA"), areas="GENE")
fileToRead <- semseeker:::file_path_build(inferenceFolder, "3_Phenotest_gaussian_Covariates1_Covariates2", extension = "csv")
localFileRes <- read.table(fileToRead, sep=";")
testthat::expect_true(nrow(localFileRes)>0)
####################################################################################
inferenceFolder <- file.path(tempFolder,"Inference")
inference_details <- expand.grid("independent_variable"= "Phenotest",
"covariates"=c("Covariates1+Covariates2"),
"family_test"=c("poisson"),
"transformation"="",
"depth_analysis"=3,
"filter_p_value" = FALSE)
association_analysis(inference_details = inference_details, result_folder = tempFolder, parallel_strategy=parallel_strategy,figures="BOTH",
markers=c("DELTAS","DELTAQ"), areas="PROBE")
fileToRead <- semseeker:::file_path_build(inferenceFolder, "3_Phenotest_poisson_Covariates1_Covariates2", extension = "csv")
localFileRes <- read.table(fileToRead, sep=";")
testthat::expect_true(nrow(localFileRes)>0)
####################################################################################
inferenceFolder <- file.path(tempFolder,"Inference")
inference_details <- expand.grid("independent_variable"= "Phenotest",
"covariates"=c("Covariates1+Covariates2"),
"family_test"=c("quantreg_0.5_5_10_0.9"),
"transformation"="scale",
"depth_analysis"=3,
"filter_p_value" = FALSE)
association_analysis(inference_details = inference_details, result_folder = tempFolder, parallel_strategy=parallel_strategy,figures="BOTH",
markers=c("DELTAS","DELTAQ"), areas="PROBE")
fileToRead <- semseeker:::file_path_build(inferenceFolder, "3_Phenotest_scale_quantreg_0.5_5_10_0.9_Covariates1_Covariates2", extension = "csv")
localFileRes <- read.table(fileToRead, sep=";")
testthat::expect_true(nrow(localFileRes)>0)
####################################################################################
inference_details <- expand.grid("independent_variable"= "Covariates1",
"covariates"=c("Phenotest+Covariates2"),
"family_test"=c("quantreg_0.5_5_10"),
"transformation"="scale",
"depth_analysis"=3,
"filter_p_value" = FALSE)
# inference_details,result_folder, maxResources, parallel_strategy
# test with area selection
association_analysis(inference_details = inference_details, result_folder = tempFolder, parallel_strategy=parallel_strategy, figures="BOTH",
markers=c("DELTAS","DELTAQ"), areas="CHR",areas_selection=c("chr1","chr2"))
fileToRead <- semseeker:::file_path_build(inferenceFolder, "3_Covariates1_scale_quantreg_0.5_5_10_Phenotest_Covariates2", extension = "csv")
localFileRes <- read.table(fileToRead, sep=";")
firstRun <- nrow(localFileRes)
testthat::expect_true(nrow(localFileRes)>0)
####################################################################################
# inference_details,result_folder, maxResources, parallel_strategy
association_analysis(inference_details = inference_details, result_folder = tempFolder, parallel_strategy=parallel_strategy, figures="BOTH",
markers=c("DELTAS","DELTAQ"), areas="PROBE")
fileToRead <- semseeker:::file_path_build(inferenceFolder, "3_Covariates1_scale_quantreg_0.5_5_10_Phenotest_Covariates2", extension = "csv")
localFileRes <- read.table(fileToRead, sep=";")
testthat::expect_true(nrow(localFileRes)>0)
secondRun <- nrow(localFileRes)
testthat::expect_true(secondRun > firstRun)
####################################################################################
inference_details <- expand.grid("independent_variable"= "Phenotest",
"covariates"=c("Covariates1+Covariates2"),
"family_test"=c("quantreg_0.5"),
"transformation"="scale",
"depth_analysis"=3,
"filter_p_value" = FALSE)
# inference_details,result_folder, maxResources, parallel_strategy
association_analysis(inference_details = inference_details, result_folder = tempFolder, parallel_strategy=parallel_strategy, figures="BOTH", markers=c("DELTAS","DELTAQ"),
areas="PROBE")
fileToRead <- semseeker:::file_path_build(inferenceFolder, "3_Phenotest_scale_quantreg_0.5_Covariates1_Covariates2", extension = "csv")
localFileRes <- read.table(fileToRead, sep=";")
testthat::expect_true(nrow(localFileRes)>0)
####################################################################################
# inference_details <- expand.grid("independent_variable"= "Phenotest",
# "covariates"=c("Covariates1+Covariates2"),
# "family_test"=c("quantreg_0.5"),
# "transformation"="scale",
# "depth_analysis"=3,
# "filter_p_value" = FALSE)
#
# # inference_details,result_folder, maxResources, parallel_strategy
# association_analysis(inference_details = inference_details, result_folder = tempFolder, parallel_strategy=parallel_strategy,
# figures="BOTH", markers=c("DELTAS","DELTAQ"), areas="PROBE")
#
# fileToRead <- semseeker:::file_path_build(inferenceFolder, "3_Phenotest_scale_quantreg_0.5_Covariates1_Covariates2", extension = "csv")
# localFileRes <- read.table(fileToRead, sep=";")
# testthat::expect_true(nrow(localFileRes)>0)
####################################################################################
inference_details <- expand.grid("independent_variable"= "Phenotest",
"covariates"=c("Covariates1+Covariates2"),
"family_test"=c("quantreg_0.5_5_10_0.99"),
"transformation"="scale",
"depth_analysis"=3,
"filter_p_value" = FALSE)
association_analysis(inference_details = inference_details, result_folder = tempFolder, parallel_strategy=parallel_strategy, figures="BOTH", markers=c("DELTAS","DELTAQ"), areas="PROBE")
fileToRead <- semseeker:::file_path_build(inferenceFolder, "3_Phenotest_scale_quantreg_0.5_5_10_0.99_Covariates1_Covariates2", extension = "csv")
localFileRes <- read.table(fileToRead, sep=";")
testthat::expect_true(nrow(localFileRes)>0)
####################################################################################
inference_details <- expand.grid("independent_variable"= "Phenotest",
"covariates"=c("Covariates1+Covariates2"),
"family_test"=c("quantreg_0.5_5_10_0.99_np"),
"transformation"="scale",
"depth_analysis"=3,
"filter_p_value" = FALSE)
association_analysis(inference_details = inference_details, result_folder = tempFolder, parallel_strategy=parallel_strategy, figures="BOTH", markers=c("DELTAS","DELTAQ"), areas="PROBE")
fileToRead <- semseeker:::file_path_build(inferenceFolder, "3_Phenotest_scale_quantreg_0.5_5_10_0.99_np_Covariates1_Covariates2", extension = "csv")
localFileRes <- read.table(fileToRead, sep=";")
testthat::expect_true(nrow(localFileRes)>0)
####################################################################################
#todo: test incremental association analysis
inference_details <- expand.grid("independent_variable"= "Phenotest",
"covariates"=c("Covariates1+Covariates2"),
"family_test"=c("quantreg_0.5_5_10_0.9"),
"transformation"="scale",
"depth_analysis"=3,
"filter_p_value" = FALSE)
association_analysis(inference_details = inference_details, result_folder = tempFolder, parallel_strategy=parallel_strategy, figures="BOTH", markers=c("DELTAS","DELTAQ"), areas="CHR")
fileToRead <- semseeker:::file_path_build(inferenceFolder, "3_Phenotest_scale_quantreg_0.5_5_10_0.9_Covariates1_Covariates2", extension = "csv")
localFileRes <- read.table(fileToRead, sep=";")
test_both <- nrow(localFileRes)
testthat::expect_true(nrow(localFileRes)>0)
####################################################################################
inference_details <- expand.grid("independent_variable"= "Group",
"covariates"="",
"family_test"=c("wilcoxon"),
"transformation"="log",
"depth_analysis"=1,
"filter_p_value" = FALSE)
association_analysis(inference_details = inference_details, result_folder = tempFolder, parallel_strategy=parallel_strategy, areas="PROBE")
fileToRead <- semseeker:::file_path_build(inferenceFolder, "1_Group_log_wilcoxon_", extension = "csv")
localFileRes <- read.table(fileToRead, sep=";")
testthat::expect_true(nrow(localFileRes)>0)
####################################################################################
inference_details <- expand.grid("independent_variable"= "Group",
"covariates"="",
"family_test"=c("t.test"),
"transformation"="log",
"depth_analysis"=1,
"filter_p_value" = FALSE)
association_analysis(inference_details = inference_details, result_folder = tempFolder, parallel_strategy=parallel_strategy, areas="PROBE")
fileToRead <- semseeker:::file_path_build(inferenceFolder, "1_Group_log_wilcoxon_", extension = "csv")
localFileRes <- read.table(fileToRead, sep=";")
testthat::expect_true(nrow(localFileRes)>0)
####################################################################################
inference_details <- expand.grid("independent_variable"= "Group",
"covariates"="",
"family_test"=c("pearson"),
"transformation"="log",
"depth_analysis"=1,
"filter_p_value" = FALSE)
association_analysis(inference_details = inference_details, result_folder = tempFolder, parallel_strategy=parallel_strategy, areas="PROBE")
fileToRead <- semseeker:::file_path_build(inferenceFolder, "1_Group_log_pearson_", extension = "csv")
localFileRes <- read.table(fileToRead, sep=";")
testthat::expect_true(nrow(localFileRes)>0)
####################################################################################
inference_details <- expand.grid("independent_variable"= "Group",
"covariates"="",
"family_test"=c("wilcoxon"),
"transformation"="quantile_5",
"depth_analysis"=1,
"filter_p_value" = FALSE)
association_analysis(inference_details = inference_details, result_folder = tempFolder, parallel_strategy=parallel_strategy, areas="PROBE")
fileToRead <- semseeker:::file_path_build(inferenceFolder, "1_Group_quantile_5_wilcoxon_", extension = "csv")
localFileRes <- read.table(fileToRead, sep=";")
testthat::expect_true(nrow(localFileRes)>0)
####################################################################################
inference_details <- expand.grid("independent_variable"= "Group",
"covariates"="",
"family_test"=c("wilcoxon"),
"transformation"="quantile_5",
"depth_analysis"=3,
"filter_p_value" = FALSE)
association_analysis(inference_details = inference_details, result_folder = tempFolder, parallel_strategy=parallel_strategy, figures="HYPER", markers="DELTAS", areas="PROBE")
fileToRead <- semseeker:::file_path_build(inferenceFolder, "3_Group_quantile_5_wilcoxon_", extension = "csv")
localFileRes <- read.table(fileToRead, sep=";")
testthat::expect_true(nrow(localFileRes)>0)
####################################################################################
inference_details <- expand.grid("independent_variable"= "Phenotest",
"covariates" =c("Covariates1+Covariates2"),
"family_test"=c("gaussian"),
"transformation"="scale",
"depth_analysis"=1,
"filter_p_value" = FALSE)
association_analysis(inference_details = inference_details, result_folder = tempFolder, parallel_strategy=parallel_strategy, figures="HYPER", markers="DELTAS", areas="GENE")
fileToRead <- semseeker:::file_path_build(inferenceFolder, "1_Phenotest_scale_gaussian_Covariates1_Covariates2", extension = "csv")
localFileRes <- read.table(fileToRead, sep=";")
testthat::expect_true(nrow(localFileRes)>0)
####################################################################################
inference_details <- expand.grid("independent_variable"= "Phenotest",
"covariates"=c("Covariates1+Covariates2"),
"family_test"=c("gaussian"),
"transformation"="scale",
"depth_analysis"=3,
"filter_p_value" = FALSE)
# inference_details,result_folder, maxResources, parallel_strategy
association_analysis(inference_details = inference_details, result_folder = tempFolder, parallel_strategy=parallel_strategy, figures="HYPER", markers="DELTAS", areas="GENE")
fileToRead <- semseeker:::file_path_build(inferenceFolder, "3_Phenotest_scale_gaussian_Covariates1_Covariates2", extension = "csv")
localFileRes <- read.table(fileToRead, sep=";")
testthat::expect_true(nrow(localFileRes)>0)
####################################################################################
inference_details <- expand.grid("independent_variable"= "Phenotest",
"covariates"=c("Covariates1+Covariates2"),
"family_test"=c("gaussian"),
"transformation"="log10",
"depth_analysis"=2,
"filter_p_value" = FALSE)
# inference_details,result_folder, maxResources, parallel_strategy
association_analysis(inference_details = inference_details, result_folder = tempFolder, parallel_strategy=parallel_strategy, areas="GENE")
fileToRead <- semseeker:::file_path_build(inferenceFolder, "2_Phenotest_log10_gaussian_Covariates1_Covariates2", extension = "csv")
localFileRes <- read.table(fileToRead, sep=";")
testthat::expect_true(nrow(localFileRes)>0)
####################################################################################
inference_details <- expand.grid("independent_variable"= "Phenotest",
"covariates"=c("Covariates1+Covariates2"),
"family_test"=c("gaussian"),
"transformation"="logn",
"depth_analysis"=3,
"filter_p_value" = FALSE)
areas_selection <- rownames(methylation_data)[1:100]
# inference_details,result_folder, maxResources, parallel_strategy
association_analysis(inference_details = inference_details, result_folder = tempFolder, parallel_strategy=parallel_strategy, areas_selection=areas_selection, areas="PROBE")
fileToRead <- semseeker:::file_path_build(inferenceFolder, "3_Phenotest_logn_gaussian_Covariates1_Covariates2", extension = "csv")
localFileRes <- read.table(fileToRead, sep=";")
testthat::expect_true(nrow(localFileRes)>0)
####################################################################################
unlink(tempFolder,recursive = TRUE)
semseeker:::close_env()
})
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test_that("association_analysis", {
####################################################################################
semseeker( sample_sheet = mySampleSheet,methylation_data = methylation_data,result_folder = tempFolder,parallel_strategy=parallel_strategy, figures="BOTH",
markers=c("BETA"), areas=c("PROBE","CHR","GENE"))
####################################################################################
inferenceFolder <- file.path(tempFolder,"Inference")
inference_details <- expand.grid("independent_variable"= "Phenotest",
"covariates"=c("Covariates1+Covariates2"),
"family_test"=c("gaussian"),
"transformation"="",
"depth_analysis"=3,
"filter_p_value" = FALSE)
association_analysis(inference_details = inference_details, result_folder = tempFolder, parallel_strategy=parallel_strategy,figures="BOTH",
markers=c("DELTAS","DELTAQ","BETA"), areas="GENE")
fileToRead <- semseeker:::file_path_build(inferenceFolder, "3_Phenotest_gaussian_Covariates1_Covariates2", extension = "csv")
localFileRes <- read.table(fileToRead, sep=";")
testthat::expect_true(nrow(localFileRes)>0)
####################################################################################
inferenceFolder <- file.path(tempFolder,"Inference")
inference_details <- expand.grid("independent_variable"= "Phenotest",
"covariates"=c("Covariates1+Covariates2"),
"family_test"=c("poisson"),
"transformation"="",
"depth_analysis"=3,
"filter_p_value" = FALSE)
association_analysis(inference_details = inference_details, result_folder = tempFolder, parallel_strategy=parallel_strategy,figures="BOTH",
markers=c("DELTAS","DELTAQ"), areas="PROBE")
fileToRead <- semseeker:::file_path_build(inferenceFolder, "3_Phenotest_poisson_Covariates1_Covariates2", extension = "csv")
localFileRes <- read.table(fileToRead, sep=";")
testthat::expect_true(nrow(localFileRes)>0)
####################################################################################
inferenceFolder <- file.path(tempFolder,"Inference")
inference_details <- expand.grid("independent_variable"= "Phenotest",
"covariates"=c("Covariates1+Covariates2"),
"family_test"=c("quantreg_0.5_5_10_0.9"),
"transformation"="scale",
"depth_analysis"=3,
"filter_p_value" = FALSE)
association_analysis(inference_details = inference_details, result_folder = tempFolder, parallel_strategy=parallel_strategy,figures="BOTH",
markers=c("DELTAS","DELTAQ"), areas="PROBE")
fileToRead <- semseeker:::file_path_build(inferenceFolder, "3_Phenotest_scale_quantreg_0.5_5_10_0.9_Covariates1_Covariates2", extension = "csv")
localFileRes <- read.table(fileToRead, sep=";")
testthat::expect_true(nrow(localFileRes)>0)
####################################################################################
inference_details <- expand.grid("independent_variable"= "Covariates1",
"covariates"=c("Phenotest+Covariates2"),
"family_test"=c("quantreg_0.5_5_10"),
"transformation"="scale",
"depth_analysis"=3,
"filter_p_value" = FALSE)
# inference_details,result_folder, maxResources, parallel_strategy
# test with area selection
association_analysis(inference_details = inference_details, result_folder = tempFolder, parallel_strategy=parallel_strategy, figures="BOTH",
markers=c("DELTAS","DELTAQ"), areas="CHR",areas_selection=c("chr1","chr2"))
fileToRead <- semseeker:::file_path_build(inferenceFolder, "3_Covariates1_scale_quantreg_0.5_5_10_Phenotest_Covariates2", extension = "csv")
localFileRes <- read.table(fileToRead, sep=";")
firstRun <- nrow(localFileRes)
testthat::expect_true(nrow(localFileRes)>0)
####################################################################################
# inference_details,result_folder, maxResources, parallel_strategy
association_analysis(inference_details = inference_details, result_folder = tempFolder, parallel_strategy=parallel_strategy, figures="BOTH",
markers=c("DELTAS","DELTAQ"), areas="PROBE")
fileToRead <- semseeker:::file_path_build(inferenceFolder, "3_Covariates1_scale_quantreg_0.5_5_10_Phenotest_Covariates2", extension = "csv")
localFileRes <- read.table(fileToRead, sep=";")
testthat::expect_true(nrow(localFileRes)>0)
secondRun <- nrow(localFileRes)
testthat::expect_true(secondRun > firstRun)
####################################################################################
inference_details <- expand.grid("independent_variable"= "Phenotest",
"covariates"=c("Covariates1+Covariates2"),
"family_test"=c("quantreg_0.5"),
"transformation"="scale",
"depth_analysis"=3,
"filter_p_value" = FALSE)
# inference_details,result_folder, maxResources, parallel_strategy
association_analysis(inference_details = inference_details, result_folder = tempFolder, parallel_strategy=parallel_strategy, figures="BOTH", markers=c("DELTAS","DELTAQ"),
areas="PROBE")
fileToRead <- semseeker:::file_path_build(inferenceFolder, "3_Phenotest_scale_quantreg_0.5_Covariates1_Covariates2", extension = "csv")
localFileRes <- read.table(fileToRead, sep=";")
testthat::expect_true(nrow(localFileRes)>0)
####################################################################################
# inference_details <- expand.grid("independent_variable"= "Phenotest",
# "covariates"=c("Covariates1+Covariates2"),
# "family_test"=c("quantreg_0.5"),
# "transformation"="scale",
# "depth_analysis"=3,
# "filter_p_value" = FALSE)
#
# # inference_details,result_folder, maxResources, parallel_strategy
# association_analysis(inference_details = inference_details, result_folder = tempFolder, parallel_strategy=parallel_strategy,
# figures="BOTH", markers=c("DELTAS","DELTAQ"), areas="PROBE")
#
# fileToRead <- semseeker:::file_path_build(inferenceFolder, "3_Phenotest_scale_quantreg_0.5_Covariates1_Covariates2", extension = "csv")
# localFileRes <- read.table(fileToRead, sep=";")
# testthat::expect_true(nrow(localFileRes)>0)
####################################################################################
inference_details <- expand.grid("independent_variable"= "Phenotest",
"covariates"=c("Covariates1+Covariates2"),
"family_test"=c("quantreg_0.5_5_10_0.99"),
"transformation"="scale",
"depth_analysis"=3,
"filter_p_value" = FALSE)
association_analysis(inference_details = inference_details, result_folder = tempFolder, parallel_strategy=parallel_strategy, figures="BOTH", markers=c("DELTAS","DELTAQ"), areas="PROBE")
fileToRead <- semseeker:::file_path_build(inferenceFolder, "3_Phenotest_scale_quantreg_0.5_5_10_0.99_Covariates1_Covariates2", extension = "csv")
localFileRes <- read.table(fileToRead, sep=";")
testthat::expect_true(nrow(localFileRes)>0)
####################################################################################
inference_details <- expand.grid("independent_variable"= "Phenotest",
"covariates"=c("Covariates1+Covariates2"),
"family_test"=c("quantreg_0.5_5_10_0.99_np"),
"transformation"="scale",
"depth_analysis"=3,
"filter_p_value" = FALSE)
association_analysis(inference_details = inference_details, result_folder = tempFolder, parallel_strategy=parallel_strategy, figures="BOTH", markers=c("DELTAS","DELTAQ"), areas="PROBE")
fileToRead <- semseeker:::file_path_build(inferenceFolder, "3_Phenotest_scale_quantreg_0.5_5_10_0.99_np_Covariates1_Covariates2", extension = "csv")
localFileRes <- read.table(fileToRead, sep=";")
testthat::expect_true(nrow(localFileRes)>0)
####################################################################################
#todo: test incremental association analysis
inference_details <- expand.grid("independent_variable"= "Phenotest",
"covariates"=c("Covariates1+Covariates2"),
"family_test"=c("quantreg_0.5_5_10_0.9"),
"transformation"="scale",
"depth_analysis"=3,
"filter_p_value" = FALSE)
association_analysis(inference_details = inference_details, result_folder = tempFolder, parallel_strategy=parallel_strategy, figures="BOTH", markers=c("DELTAS","DELTAQ"), areas="CHR")
fileToRead <- semseeker:::file_path_build(inferenceFolder, "3_Phenotest_scale_quantreg_0.5_5_10_0.9_Covariates1_Covariates2", extension = "csv")
localFileRes <- read.table(fileToRead, sep=";")
test_both <- nrow(localFileRes)
testthat::expect_true(nrow(localFileRes)>0)
####################################################################################
inference_details <- expand.grid("independent_variable"= "Group",
"covariates"="",
"family_test"=c("wilcoxon"),
"transformation"="log",
"depth_analysis"=1,
"filter_p_value" = FALSE)
association_analysis(inference_details = inference_details, result_folder = tempFolder, parallel_strategy=parallel_strategy, areas="PROBE")
fileToRead <- semseeker:::file_path_build(inferenceFolder, "1_Group_log_wilcoxon_", extension = "csv")
localFileRes <- read.table(fileToRead, sep=";")
testthat::expect_true(nrow(localFileRes)>0)
####################################################################################
inference_details <- expand.grid("independent_variable"= "Group",
"covariates"="",
"family_test"=c("t.test"),
"transformation"="log",
"depth_analysis"=1,
"filter_p_value" = FALSE)
association_analysis(inference_details = inference_details, result_folder = tempFolder, parallel_strategy=parallel_strategy, areas="PROBE")
fileToRead <- semseeker:::file_path_build(inferenceFolder, "1_Group_log_wilcoxon_", extension = "csv")
localFileRes <- read.table(fileToRead, sep=";")
testthat::expect_true(nrow(localFileRes)>0)
####################################################################################
inference_details <- expand.grid("independent_variable"= "Group",
"covariates"="",
"family_test"=c("pearson"),
"transformation"="log",
"depth_analysis"=1,
"filter_p_value" = FALSE)
association_analysis(inference_details = inference_details, result_folder = tempFolder, parallel_strategy=parallel_strategy, areas="PROBE")
fileToRead <- semseeker:::file_path_build(inferenceFolder, "1_Group_log_pearson_", extension = "csv")
localFileRes <- read.table(fileToRead, sep=";")
testthat::expect_true(nrow(localFileRes)>0)
####################################################################################
inference_details <- expand.grid("independent_variable"= "Group",
"covariates"="",
"family_test"=c("wilcoxon"),
"transformation"="quantile_5",
"depth_analysis"=1,
"filter_p_value" = FALSE)
association_analysis(inference_details = inference_details, result_folder = tempFolder, parallel_strategy=parallel_strategy, areas="PROBE")
fileToRead <- semseeker:::file_path_build(inferenceFolder, "1_Group_quantile_5_wilcoxon_", extension = "csv")
localFileRes <- read.table(fileToRead, sep=";")
testthat::expect_true(nrow(localFileRes)>0)
####################################################################################
inference_details <- expand.grid("independent_variable"= "Group",
"covariates"="",
"family_test"=c("wilcoxon"),
"transformation"="quantile_5",
"depth_analysis"=3,
"filter_p_value" = FALSE)
association_analysis(inference_details = inference_details, result_folder = tempFolder, parallel_strategy=parallel_strategy, figures="HYPER", markers="DELTAS", areas="PROBE")
fileToRead <- semseeker:::file_path_build(inferenceFolder, "3_Group_quantile_5_wilcoxon_", extension = "csv")
localFileRes <- read.table(fileToRead, sep=";")
testthat::expect_true(nrow(localFileRes)>0)
####################################################################################
inference_details <- expand.grid("independent_variable"= "Phenotest",
"covariates" =c("Covariates1+Covariates2"),
"family_test"=c("gaussian"),
"transformation"="scale",
"depth_analysis"=1,
"filter_p_value" = FALSE)
association_analysis(inference_details = inference_details, result_folder = tempFolder, parallel_strategy=parallel_strategy, figures="HYPER", markers="DELTAS", areas="GENE")
fileToRead <- semseeker:::file_path_build(inferenceFolder, "1_Phenotest_scale_gaussian_Covariates1_Covariates2", extension = "csv")
localFileRes <- read.table(fileToRead, sep=";")
testthat::expect_true(nrow(localFileRes)>0)
####################################################################################
inference_details <- expand.grid("independent_variable"= "Phenotest",
"covariates"=c("Covariates1+Covariates2"),
"family_test"=c("gaussian"),
"transformation"="scale",
"depth_analysis"=3,
"filter_p_value" = FALSE)
# inference_details,result_folder, maxResources, parallel_strategy
association_analysis(inference_details = inference_details, result_folder = tempFolder, parallel_strategy=parallel_strategy, figures="HYPER", markers="DELTAS", areas="GENE")
fileToRead <- semseeker:::file_path_build(inferenceFolder, "3_Phenotest_scale_gaussian_Covariates1_Covariates2", extension = "csv")
localFileRes <- read.table(fileToRead, sep=";")
testthat::expect_true(nrow(localFileRes)>0)
####################################################################################
inference_details <- expand.grid("independent_variable"= "Phenotest",
"covariates"=c("Covariates1+Covariates2"),
"family_test"=c("gaussian"),
"transformation"="log10",
"depth_analysis"=2,
"filter_p_value" = FALSE)
# inference_details,result_folder, maxResources, parallel_strategy
association_analysis(inference_details = inference_details, result_folder = tempFolder, parallel_strategy=parallel_strategy, areas="GENE")
fileToRead <- semseeker:::file_path_build(inferenceFolder, "2_Phenotest_log10_gaussian_Covariates1_Covariates2", extension = "csv")
localFileRes <- read.table(fileToRead, sep=";")
testthat::expect_true(nrow(localFileRes)>0)
####################################################################################
inference_details <- expand.grid("independent_variable"= "Phenotest",
"covariates"=c("Covariates1+Covariates2"),
"family_test"=c("gaussian"),
"transformation"="logn",
"depth_analysis"=3,
"filter_p_value" = FALSE)
areas_selection <- rownames(methylation_data)[1:100]
# inference_details,result_folder, maxResources, parallel_strategy
association_analysis(inference_details = inference_details, result_folder = tempFolder, parallel_strategy=parallel_strategy, areas_selection=areas_selection, areas="PROBE")
fileToRead <- semseeker:::file_path_build(inferenceFolder, "3_Phenotest_logn_gaussian_Covariates1_Covariates2", extension = "csv")
localFileRes <- read.table(fileToRead, sep=";")
testthat::expect_true(nrow(localFileRes)>0)
####################################################################################
unlink(tempFolder,recursive = TRUE)
semseeker:::close_env()
})
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