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dataset_pipeline_arguments.R
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dataset_pipeline_arguments.R
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dataset_pipeline_arguments <- list(
#1
#GBM1 GBMVsCont
#filter <- expression(Age > 55 & Sex == 'M')
list(phenotype_file_name = "phenotype_info/phenotype_GBM1.txt",
read_count_dir_path = "data/GBM/1",
read_count_file_name = "GSE122488_normalized_microRNA_counts.txt",
skip_row_count = 3,
filter_expression = expression(TRUE),
dataset_id = "GBM1",
classification_criteria = "GBMvsCont",
classes = c("Control", "GBM"),
cores = 16,
fems_to_run = c("all", "t-test", "t-test_pval_0.025", "t-test_pval_0.01", "t-test_pval_0.005", "t-test_holm",
"t-test_bonferroni", "t-test_BH", "t-test_BY", "wilcoxontest", "wilcoxontest_pval_0.025",
"wilcoxontest_pval_0.01", "wilcoxontest_pval_0.005", "wilcoxontest_holm", "wilcoxontest_bonferroni",
"wilcoxontest_BH", "wilcoxontest_BY", "rf", "ranger_perm", "ranger_impu", "ranger_impu_cor",
"mrmr10", "mrmr20", "mrmr30", "mrmr50", "mrmr75", "mrmr100", "mrmr_perc25", "mrmr_perc50", "mrmr_perc75")),
#2
#GBM1 GBMvsGlioma
list(phenotype_file_name = "phenotype_info/phenotype_GBM1.txt",
read_count_dir_path = "data/GBM/1",
read_count_file_name = "GSE122488_normalized_microRNA_counts.txt",
skip_row_count = 3,
filter_expression = expression(TRUE),
dataset_id = "GBM1",
classification_criteria = "GBMvsGlioma",
classes = c("Glioma", "GBM"),
cores = 16,
fems_to_run = c("all", "t-test", "t-test_pval_0.025", "t-test_pval_0.01", "t-test_pval_0.005", "t-test_holm",
"t-test_bonferroni", "t-test_BH", "t-test_BY", "wilcoxontest", "wilcoxontest_pval_0.025",
"wilcoxontest_pval_0.01", "wilcoxontest_pval_0.005", "wilcoxontest_holm", "wilcoxontest_bonferroni",
"wilcoxontest_BH", "wilcoxontest_BY", "rf", "ranger_perm", "ranger_impu", "ranger_impu_cor",
"mrmr10", "mrmr20", "mrmr30", "mrmr50", "mrmr75", "mrmr100", "mrmr_perc25", "mrmr_perc50", "mrmr_perc75")),
#3
#GBM1 GliomavsCont
list(phenotype_file_name = "phenotype_info/phenotype_GBM1.txt",
read_count_dir_path = "data/GBM/1",
read_count_file_name = "GSE122488_normalized_microRNA_counts.txt",
skip_row_count = 3,
filter_expression = expression(TRUE),
dataset_id = "GBM1",
classification_criteria = "GliomavsCont",
classes = c("Control", "Glioma"),
cores = 16,
fems_to_run = c("all", "t-test", "t-test_pval_0.025", "t-test_pval_0.01", "t-test_pval_0.005", "t-test_holm",
"t-test_bonferroni", "t-test_BH", "t-test_BY", "wilcoxontest", "wilcoxontest_pval_0.025",
"wilcoxontest_pval_0.01", "wilcoxontest_pval_0.005", "wilcoxontest_holm", "wilcoxontest_bonferroni",
"wilcoxontest_BH", "wilcoxontest_BY", "rf", "ranger_perm", "ranger_impu", "ranger_impu_cor",
"mrmr10", "mrmr20", "mrmr30", "mrmr50", "mrmr75", "mrmr100", "mrmr_perc25", "mrmr_perc50", "mrmr_perc75")),
#4
#GBM2 GBMVsNC
list(phenotype_file_name = "phenotype_info/phenotype_GBM2.txt",
read_count_dir_path = "data/GBM/2",
read_count_file_name = "GSE112462.txt",
skip_row_count = 0,
filter_expression = expression(TRUE),
dataset_id = "GBM2",
classification_criteria = "GBMVsNC",
classes = c("NonCancer", "GBM"),
cores = 16,
fems_to_run = c("all", "t-test", "t-test_pval_0.025", "t-test_pval_0.01", "t-test_pval_0.005", "t-test_holm",
"t-test_bonferroni", "t-test_BH", "t-test_BY", "wilcoxontest", "wilcoxontest_pval_0.025",
"wilcoxontest_pval_0.01", "wilcoxontest_pval_0.005", "wilcoxontest_holm", "wilcoxontest_bonferroni",
"wilcoxontest_BH", "wilcoxontest_BY", "rf", "ranger_perm", "ranger_impu", "ranger_impu_cor",
"mrmr10", "mrmr20", "mrmr30", "mrmr50", "mrmr75", "mrmr100", "mrmr_perc25", "mrmr_perc50", "mrmr_perc75")),
#5
#GBM2 GBMVsAstro_Oligo
list(phenotype_file_name = "phenotype_info/phenotype_GBM2.txt",
read_count_dir_path = "data/GBM/2",
read_count_file_name = "GSE112462.txt",
skip_row_count = 0,
filter_expression = expression(TRUE),
dataset_id = "GBM2",
classification_criteria = "GBMVsAstro_Oligo",
classes = c("Astro_Oligo", "GBM"),
cores = 16,
fems_to_run = c("all", "t-test", "t-test_pval_0.025", "t-test_pval_0.01", "t-test_pval_0.005", "t-test_holm",
"t-test_bonferroni", "t-test_BH", "t-test_BY", "wilcoxontest", "wilcoxontest_pval_0.025",
"wilcoxontest_pval_0.01", "wilcoxontest_pval_0.005", "wilcoxontest_holm", "wilcoxontest_bonferroni",
"wilcoxontest_BH", "wilcoxontest_BY", "rf", "ranger_perm", "ranger_impu", "ranger_impu_cor",
"mrmr10", "mrmr20", "mrmr30", "mrmr50", "mrmr75", "mrmr100", "mrmr_perc25", "mrmr_perc50", "mrmr_perc75")),
#6
#GBM2 Astro_OligoVsNC
list(phenotype_file_name = "phenotype_info/phenotype_GBM2.txt",
read_count_dir_path = "data/GBM/2",
read_count_file_name = "GSE112462.txt",
skip_row_count = 0,
filter_expression = expression(TRUE),
dataset_id = "GBM2",
classification_criteria = "Astro_OligoVsNC",
classes = c("NonCancer", "Astro_Oligo"),
cores = 16,
fems_to_run = c("all", "t-test", "t-test_pval_0.025", "t-test_pval_0.01", "t-test_pval_0.005", "t-test_holm",
"t-test_bonferroni", "t-test_BH", "t-test_BY", "wilcoxontest", "wilcoxontest_pval_0.025",
"wilcoxontest_pval_0.01", "wilcoxontest_pval_0.005", "wilcoxontest_holm", "wilcoxontest_bonferroni",
"wilcoxontest_BH", "wilcoxontest_BY", "rf", "ranger_perm", "ranger_impu", "ranger_impu_cor",
"mrmr10", "mrmr20", "mrmr30", "mrmr50", "mrmr75", "mrmr100", "mrmr_perc25", "mrmr_perc50", "mrmr_perc75")),
#7
#LungCancer1 LUADVsControl
list(phenotype_file_name = "phenotype_info/phenotype_LungCancer1.txt",
read_count_dir_path = "data/LungCancer/1",
read_count_file_name = "GSE111803_Readcount_TPM.txt",
skip_row_count = 0,
filter_expression = expression(TRUE),
dataset_id = "LungCancer1",
classification_criteria = "LUADVsControl",
classes = c("Control", "LUAD"),
cores = 16,
fems_to_run = c("all", "t-test", "t-test_pval_0.025", "t-test_pval_0.01", "t-test_pval_0.005", "t-test_holm",
"t-test_bonferroni", "t-test_BH", "t-test_BY", "wilcoxontest", "wilcoxontest_pval_0.025",
"wilcoxontest_pval_0.01", "wilcoxontest_pval_0.005", "wilcoxontest_holm", "wilcoxontest_bonferroni",
"wilcoxontest_BH", "wilcoxontest_BY", "rf", "ranger_perm", "ranger_impu", "ranger_impu_cor",
"mrmr10", "mrmr20", "mrmr30", "mrmr50", "mrmr75", "mrmr100", "mrmr_perc25", "mrmr_perc50", "mrmr_perc75")),
#8
#LungCancer3 NSCLCVsCont
list(phenotype_file_name = "phenotype_info/phenotype_LungCancer3.txt",
read_count_dir_path = "data/LungCancer/3",
read_count_file_name = "GSE114711.txt",
skip_row_count = 0,
filter_expression = expression(TRUE),
dataset_id = "LungCancer3",
classification_criteria = "NSCLCVsCont",
classes = c("control", "NSCLC"),
cores = 16,
fems_to_run = c("all", "t-test", "t-test_pval_0.025", "t-test_pval_0.01", "t-test_pval_0.005", "t-test_holm",
"t-test_bonferroni", "t-test_BH", "t-test_BY", "wilcoxontest", "wilcoxontest_pval_0.025",
"wilcoxontest_pval_0.01", "wilcoxontest_pval_0.005", "wilcoxontest_holm", "wilcoxontest_bonferroni",
"wilcoxontest_BH", "wilcoxontest_BY", "rf", "ranger_perm", "ranger_impu", "ranger_impu_cor",
"mrmr10", "mrmr20", "mrmr30", "mrmr50", "mrmr75", "mrmr100", "mrmr_perc25", "mrmr_perc50", "mrmr_perc75")),
#9
#LungCancer3 ENSCLCVsCont
list(phenotype_file_name = "phenotype_info/phenotype_LungCancer3.txt",
read_count_dir_path = "data/LungCancer/3",
read_count_file_name = "GSE114711.txt",
skip_row_count = 0,
filter_expression = expression(TRUE),
dataset_id = "LungCancer3",
classification_criteria = "ENSCLCVsCont",
classes = c("control", "earlystageNSCLC"),
cores = 16,
fems_to_run = c("all", "t-test", "t-test_pval_0.025", "t-test_pval_0.01", "t-test_pval_0.005", "t-test_holm",
"t-test_bonferroni", "t-test_BH", "t-test_BY", "wilcoxontest", "wilcoxontest_pval_0.025",
"wilcoxontest_pval_0.01", "wilcoxontest_pval_0.005", "wilcoxontest_holm", "wilcoxontest_bonferroni",
"wilcoxontest_BH", "wilcoxontest_BY", "rf", "ranger_perm", "ranger_impu", "ranger_impu_cor",
"mrmr10", "mrmr20", "mrmr30", "mrmr50", "mrmr75", "mrmr100", "mrmr_perc25", "mrmr_perc50", "mrmr_perc75")),
#10
#LungCancer3 LNSCLCVsCont
list(phenotype_file_name = "phenotype_info/phenotype_LungCancer3.txt",
read_count_dir_path = "data/LungCancer/3",
read_count_file_name = "GSE114711.txt",
skip_row_count = 0,
filter_expression = expression(TRUE),
dataset_id = "LungCancer3",
classification_criteria = "LNSCLCVsCont",
classes = c("control", "latestageNSCLC"),
cores = 16,
fems_to_run = c("all", "t-test", "t-test_pval_0.025", "t-test_pval_0.01", "t-test_pval_0.005", "t-test_holm",
"t-test_bonferroni", "t-test_BH", "t-test_BY", "wilcoxontest", "wilcoxontest_pval_0.025",
"wilcoxontest_pval_0.01", "wilcoxontest_pval_0.005", "wilcoxontest_holm", "wilcoxontest_bonferroni",
"wilcoxontest_BH", "wilcoxontest_BY", "rf", "ranger_perm", "ranger_impu", "ranger_impu_cor",
"mrmr10", "mrmr20", "mrmr30", "mrmr50", "mrmr75", "mrmr100", "mrmr_perc25", "mrmr_perc50", "mrmr_perc75")),
#11
#LungCancer3 LNSCLCVsENSCLC
list(phenotype_file_name = "phenotype_info/phenotype_LungCancer3.txt",
read_count_dir_path = "data/LungCancer/3",
read_count_file_name = "GSE114711.txt",
skip_row_count = 0,
filter_expression = expression(TRUE),
dataset_id = "LungCancer3",
classification_criteria = "LNSCLCVsENSCLC",
classes = c("earlystageNSCLC", "latestageNSCLC"),
cores = 16,
fems_to_run = c("all", "t-test", "t-test_pval_0.025", "t-test_pval_0.01", "t-test_pval_0.005", "t-test_holm",
"t-test_bonferroni", "t-test_BH", "t-test_BY", "wilcoxontest", "wilcoxontest_pval_0.025",
"wilcoxontest_pval_0.01", "wilcoxontest_pval_0.005", "wilcoxontest_holm", "wilcoxontest_bonferroni",
"wilcoxontest_BH", "wilcoxontest_BY", "rf", "ranger_perm", "ranger_impu", "ranger_impu_cor",
"mrmr10", "mrmr20", "mrmr30", "mrmr50", "mrmr75", "mrmr100", "mrmr_perc25", "mrmr_perc50", "mrmr_perc75")),
#12
#TEP2015 GBMVsHC
list(phenotype_file_name = "phenotype_info/phenotype_TEP2015.txt",
read_count_dir_path = "data/GBM/TEP",
read_count_file_name = "GSE68086_TEP_data_matrix.txt",
skip_row_count = 0,
filter_expression = expression(TRUE),
dataset_id = "TEP2015",
classification_criteria = "GBMVsHC",
classes = c("HC", "GBM"),
cores = 16,
fems_to_run = c("all", "t-test", "t-test_pval_0.025", "t-test_pval_0.01", "t-test_pval_0.005", "t-test_holm",
"t-test_bonferroni", "t-test_BH", "t-test_BY", "wilcoxontest", "wilcoxontest_pval_0.025",
"wilcoxontest_pval_0.01", "wilcoxontest_pval_0.005", "wilcoxontest_holm", "wilcoxontest_bonferroni",
"wilcoxontest_BH", "wilcoxontest_BY", "rf", "ranger_perm", "ranger_impu", "ranger_impu_cor",
"mrmr10", "mrmr20", "mrmr30", "mrmr50", "mrmr75", "mrmr100", "mrmr_perc25", "mrmr_perc50", "mrmr_perc75")),
#13
#TEP2015 NSCLCVsHC
list(phenotype_file_name = "phenotype_info/phenotype_TEP2015.txt",
read_count_dir_path = "data/GBM/TEP",
read_count_file_name = "GSE68086_TEP_data_matrix.txt",
skip_row_count = 0,
filter_expression = expression(TRUE),
dataset_id = "TEP2015",
classification_criteria = "NSCLCVsHC",
classes = c("HC", "NSCLC"),
cores = 16,
fems_to_run = c("all", "t-test", "t-test_pval_0.025", "t-test_pval_0.01", "t-test_pval_0.005", "t-test_holm",
"t-test_bonferroni", "t-test_BH", "t-test_BY", "wilcoxontest", "wilcoxontest_pval_0.025",
"wilcoxontest_pval_0.01", "wilcoxontest_pval_0.005", "wilcoxontest_holm", "wilcoxontest_bonferroni",
"wilcoxontest_BH", "wilcoxontest_BY", "rf", "ranger_perm", "ranger_impu", "ranger_impu_cor",
"mrmr10", "mrmr20", "mrmr30", "mrmr50", "mrmr75", "mrmr100", "mrmr_perc25", "mrmr_perc50", "mrmr_perc75")),
#14
#TEP2015 CancerVsHC
#note : this failed with 100 hour execution - insufficient time
#rerunning as 30 different jobs
list(phenotype_file_name = "phenotype_info/phenotype_TEP2015.txt",
read_count_dir_path = "data/GBM/TEP",
read_count_file_name = "GSE68086_TEP_data_matrix.txt",
skip_row_count = 0,
filter_expression = expression(TRUE),
dataset_id = "TEP2015",
classification_criteria = "CancerVsHC",
classes = c("HC", "Cancer"),
cores = 16,
fems_to_run = c("all", "t-test", "t-test_pval_0.025", "t-test_pval_0.01", "t-test_pval_0.005", "t-test_holm",
"t-test_bonferroni", "t-test_BH", "t-test_BY", "wilcoxontest", "wilcoxontest_pval_0.025",
"wilcoxontest_pval_0.01", "wilcoxontest_pval_0.005", "wilcoxontest_holm", "wilcoxontest_bonferroni",
"wilcoxontest_BH", "wilcoxontest_BY", "rf", "ranger_perm", "ranger_impu", "ranger_impu_cor",
"mrmr10", "mrmr20", "mrmr30", "mrmr50", "mrmr75", "mrmr100", "mrmr_perc25", "mrmr_perc50", "mrmr_perc75")),
#15
#TEP2017 NSCLCVsNC
list(phenotype_file_name = "phenotype_info/phenotype_TEP2017.txt",
read_count_dir_path = "data/LungCancer/TEP",
read_count_file_name = "GSE89843_TEP_Count_Matrix.txt",
skip_row_count = 0,
filter_expression = expression(TRUE),
dataset_id = "TEP2017",
classification_criteria = "NSCLCVsNC",
classes = c("NonCancer", "NSCLC"),
cores = 32,
fems_to_run = c("all", "t-test", "t-test_pval_0.025", "t-test_pval_0.01", "t-test_pval_0.005", "t-test_holm",
"t-test_bonferroni", "t-test_BH", "t-test_BY", "wilcoxontest", "wilcoxontest_pval_0.025",
"wilcoxontest_pval_0.01", "wilcoxontest_pval_0.005", "wilcoxontest_holm", "wilcoxontest_bonferroni",
"wilcoxontest_BH", "wilcoxontest_BY", "rf", "ranger_perm", "ranger_impu", "ranger_impu_cor",
"mrmr10", "mrmr20", "mrmr30", "mrmr50", "mrmr75", "mrmr100", "mrmr_perc25", "mrmr_perc50", "mrmr_perc75")),
#16
#TEP2015 CRCVsHC
list(phenotype_file_name = "phenotype_info/phenotype_TEP2015.txt",
read_count_dir_path = "data/GBM/TEP",
read_count_file_name = "GSE68086_TEP_data_matrix.txt",
skip_row_count = 0,
filter_expression = expression(TRUE),
dataset_id = "TEP2015",
classification_criteria = "CRCVsHC",
classes = c("HC", "CRC"),
cores = 16,
fems_to_run = c("all", "t-test", "t-test_pval_0.025", "t-test_pval_0.01", "t-test_pval_0.005", "t-test_holm",
"t-test_bonferroni", "t-test_BH", "t-test_BY", "wilcoxontest", "wilcoxontest_pval_0.025",
"wilcoxontest_pval_0.01", "wilcoxontest_pval_0.005", "wilcoxontest_holm", "wilcoxontest_bonferroni",
"wilcoxontest_BH", "wilcoxontest_BY", "rf", "ranger_perm", "ranger_impu", "ranger_impu_cor",
"mrmr10", "mrmr20", "mrmr30", "mrmr50", "mrmr75", "mrmr100", "mrmr_perc25", "mrmr_perc50", "mrmr_perc75")),
#17
#TEP2015 BCsHC
list(phenotype_file_name = "phenotype_info/phenotype_TEP2015.txt",
read_count_dir_path = "data/GBM/TEP",
read_count_file_name = "GSE68086_TEP_data_matrix.txt",
skip_row_count = 0,
filter_expression = expression(TRUE),
dataset_id = "TEP2015",
classification_criteria = "BCVsHC",
classes = c("HC", "BC"),
cores = 16,
fems_to_run = c("all", "t-test", "t-test_pval_0.025", "t-test_pval_0.01", "t-test_pval_0.005", "t-test_holm",
"t-test_bonferroni", "t-test_BH", "t-test_BY", "wilcoxontest", "wilcoxontest_pval_0.025",
"wilcoxontest_pval_0.01", "wilcoxontest_pval_0.005", "wilcoxontest_holm", "wilcoxontest_bonferroni",
"wilcoxontest_BH", "wilcoxontest_BY", "rf", "ranger_perm", "ranger_impu", "ranger_impu_cor",
"mrmr10", "mrmr20", "mrmr30", "mrmr50", "mrmr75", "mrmr100", "mrmr_perc25", "mrmr_perc50", "mrmr_perc75")),
#18
#TEP2015 PCsHC
list(phenotype_file_name = "phenotype_info/phenotype_TEP2015.txt",
read_count_dir_path = "data/GBM/TEP",
read_count_file_name = "GSE68086_TEP_data_matrix.txt",
skip_row_count = 0,
filter_expression = expression(TRUE),
dataset_id = "TEP2015",
classification_criteria = "PCVsHC",
classes = c("HC", "PancC"),
cores = 16,
fems_to_run = c("all", "t-test", "t-test_pval_0.025", "t-test_pval_0.01", "t-test_pval_0.005", "t-test_holm",
"t-test_bonferroni", "t-test_BH", "t-test_BY", "wilcoxontest", "wilcoxontest_pval_0.025",
"wilcoxontest_pval_0.01", "wilcoxontest_pval_0.005", "wilcoxontest_holm", "wilcoxontest_bonferroni",
"wilcoxontest_BH", "wilcoxontest_BY", "rf", "ranger_perm", "ranger_impu", "ranger_impu_cor",
"mrmr10", "mrmr20", "mrmr30", "mrmr50", "mrmr75", "mrmr100", "mrmr_perc25", "mrmr_perc50", "mrmr_perc75")),
#19
#GSE71008 CRCVsHC
list(phenotype_file_name = "phenotype_info/phenotype_GSE71008.txt",
read_count_dir_path = "data/GSE71008",
read_count_file_name = "GSE71008_Data_matrix.txt",
skip_row_count = 0,
filter_expression = expression(TRUE),
dataset_id = "GSE71008",
classification_criteria = "CRCVsHC",
classes = c("HC", "CRC"),
cores = 16,
fems_to_run = c("all", "t-test", "t-test_pval_0.025", "t-test_pval_0.01", "t-test_pval_0.005", "t-test_holm",
"t-test_bonferroni", "t-test_BH", "t-test_BY", "wilcoxontest", "wilcoxontest_pval_0.025",
"wilcoxontest_pval_0.01", "wilcoxontest_pval_0.005", "wilcoxontest_holm", "wilcoxontest_bonferroni",
"wilcoxontest_BH", "wilcoxontest_BY", "rf", "ranger_perm", "ranger_impu", "ranger_impu_cor",
"mrmr10", "mrmr20", "mrmr30", "mrmr50", "mrmr75", "mrmr100", "mrmr_perc25", "mrmr_perc50", "mrmr_perc75")),
#20
#GSE83270 BCVsHC
list(phenotype_file_name = "phenotype_info/phenotype_GSE83270.txt",
read_count_dir_path = "data/GSE83270",
read_count_file_name = "GSE83270_series_matrix.txt",
skip_row_count = 57,
row_count = 2158,
filter_expression = expression(TRUE),
dataset_id = "GSE83270",
classification_criteria = "BCVsHC",
classes = c("HC", "BC"),
cores = 16,
fems_to_run = c("all", "t-test", "t-test_pval_0.025", "t-test_pval_0.01", "t-test_pval_0.005", "t-test_holm",
"t-test_bonferroni", "t-test_BH", "t-test_BY", "wilcoxontest", "wilcoxontest_pval_0.025",
"wilcoxontest_pval_0.01", "wilcoxontest_pval_0.005", "wilcoxontest_holm", "wilcoxontest_bonferroni",
"wilcoxontest_BH", "wilcoxontest_BY", "rf", "ranger_perm", "ranger_impu", "ranger_impu_cor",
"mrmr10", "mrmr20", "mrmr30", "mrmr50", "mrmr75", "mrmr100", "mrmr_perc25", "mrmr_perc50", "mrmr_perc75")),
#21
#GSE22981 EBCVsHC (Early Stage Breast Cancer Vs Healthy Control)
list(phenotype_file_name = "phenotype_info/phenotype_GSE22981.txt",
read_count_dir_path = "data/GSE22981",
read_count_file_name = "GSE22981_series_matrix.txt",
skip_row_count = 64,
row_count = 1145,
filter_expression = expression(TRUE),
dataset_id = "GSE22981",
classification_criteria = "EBCVsHC",
classes = c("HC", "EBC"),
cores = 16,
fems_to_run = c("all", "t-test", "t-test_pval_0.025", "t-test_pval_0.01", "t-test_pval_0.005", "t-test_holm",
"t-test_bonferroni", "t-test_BH", "t-test_BY", "wilcoxontest", "wilcoxontest_pval_0.025",
"wilcoxontest_pval_0.01", "wilcoxontest_pval_0.005", "wilcoxontest_holm", "wilcoxontest_bonferroni",
"wilcoxontest_BH", "wilcoxontest_BY", "rf", "ranger_perm", "ranger_impu", "ranger_impu_cor",
"mrmr10", "mrmr20", "mrmr30", "mrmr50", "mrmr75", "mrmr100", "mrmr_perc25", "mrmr_perc50", "mrmr_perc75")),
#22
#GSE73002 BCVsNC
list(phenotype_file_name = "phenotype_info/phenotype_GSE73002.txt",
read_count_dir_path = "data/GSE73002",
read_count_file_name = "GSE73002_series_matrix.txt",
skip_row_count = 73,
row_count = 2540,
na_strings = "null",
filter_expression = expression(TRUE),
dataset_id = "GSE73002",
classification_criteria = "BCVsNC",
classes = c("NC", "BC"),
cores = 32,
fems_to_run = c("all", "t-test", "t-test_pval_0.025", "t-test_pval_0.01", "t-test_pval_0.005", "t-test_holm",
"t-test_bonferroni", "t-test_BH", "t-test_BY", "wilcoxontest", "wilcoxontest_pval_0.025",
"wilcoxontest_pval_0.01", "wilcoxontest_pval_0.005", "wilcoxontest_holm", "wilcoxontest_bonferroni",
"wilcoxontest_BH", "wilcoxontest_BY", "rf", "ranger_perm", "ranger_impu", "ranger_impu_cor",
"mrmr10", "mrmr20", "mrmr30", "mrmr50", "mrmr75", "mrmr100", "mrmr_perc25", "mrmr_perc50", "mrmr_perc75")),
#23
#GSE44281 BCVsNC
list(phenotype_file_name = "phenotype_info/phenotype_GSE44281.txt",
read_count_dir_path = "data/GSE44281",
read_count_file_name = "GSE44281_series_matrix.txt",
skip_row_count = 67,
row_count = 20180,
filter_expression = expression(TRUE),
dataset_id = "GSE44281",
classification_criteria = "caseVsnoncase",
classes = c("noncase", "case"),
cores = 32,
fems_to_run = c("all", "t-test", "t-test_pval_0.025", "t-test_pval_0.01", "t-test_pval_0.005", "t-test_holm",
"t-test_bonferroni", "t-test_BH", "t-test_BY", "wilcoxontest", "wilcoxontest_pval_0.025",
"wilcoxontest_pval_0.01", "wilcoxontest_pval_0.005", "wilcoxontest_holm", "wilcoxontest_bonferroni",
"wilcoxontest_BH", "wilcoxontest_BY", "rf", "ranger_perm", "ranger_impu", "ranger_impu_cor",
"mrmr10", "mrmr20", "mrmr30", "mrmr50", "mrmr75", "mrmr100", "mrmr_perc25", "mrmr_perc50", "mrmr_perc75")),
##################
#ga_rf executions
#1
#GBM1 GBMVsCont
#filter <- expression(Age > 55 & Sex == 'M')
list(phenotype_file_name = "phenotype_info/phenotype_GBM1.txt",
read_count_dir_path = "data/GBM/1",
read_count_file_name = "GSE122488_normalized_microRNA_counts.txt",
skip_row_count = 3,
filter_expression = expression(TRUE),
dataset_id = "GBM1",
classification_criteria = "GBMvsCont",
classes = c("Control", "GBM"),
cores = 16,
fems_to_run = c("ga_rf")),
#2
#GBM1 GBMvsGlioma
list(phenotype_file_name = "phenotype_info/phenotype_GBM1.txt",
read_count_dir_path = "data/GBM/1",
read_count_file_name = "GSE122488_normalized_microRNA_counts.txt",
skip_row_count = 3,
filter_expression = expression(TRUE),
dataset_id = "GBM1",
classification_criteria = "GBMvsGlioma",
classes = c("Glioma", "GBM"),
cores = 16,
fems_to_run = c("ga_rf")),
#3
#GBM1 GliomavsCont
list(phenotype_file_name = "phenotype_info/phenotype_GBM1.txt",
read_count_dir_path = "data/GBM/1",
read_count_file_name = "GSE122488_normalized_microRNA_counts.txt",
skip_row_count = 3,
filter_expression = expression(TRUE),
dataset_id = "GBM1",
classification_criteria = "GliomavsCont",
classes = c("Control", "Glioma"),
cores = 16,
fems_to_run = c("ga_rf")),
#4
#GBM2 GBMVsNC
list(phenotype_file_name = "phenotype_info/phenotype_GBM2.txt",
read_count_dir_path = "data/GBM/2",
read_count_file_name = "GSE112462.txt",
skip_row_count = 0,
filter_expression = expression(TRUE),
dataset_id = "GBM2",
classification_criteria = "GBMVsNC",
classes = c("NonCancer", "GBM"),
cores = 16,
fems_to_run = c("ga_rf")),
#5
#GBM2 GBMVsAstro_Oligo
list(phenotype_file_name = "phenotype_info/phenotype_GBM2.txt",
read_count_dir_path = "data/GBM/2",
read_count_file_name = "GSE112462.txt",
skip_row_count = 0,
filter_expression = expression(TRUE),
dataset_id = "GBM2",
classification_criteria = "GBMVsAstro_Oligo",
classes = c("Astro_Oligo", "GBM"),
cores = 16,
fems_to_run = c("ga_rf")),
#6
#GBM2 Astro_OligoVsNC
list(phenotype_file_name = "phenotype_info/phenotype_GBM2.txt",
read_count_dir_path = "data/GBM/2",
read_count_file_name = "GSE112462.txt",
skip_row_count = 0,
filter_expression = expression(TRUE),
dataset_id = "GBM2",
classification_criteria = "Astro_OligoVsNC",
classes = c("NonCancer", "Astro_Oligo"),
cores = 16,
fems_to_run = c("ga_rf")),
#7
#LungCancer1 LUADVsControl
list(phenotype_file_name = "phenotype_info/phenotype_LungCancer1.txt",
read_count_dir_path = "data/LungCancer/1",
read_count_file_name = "GSE111803_Readcount_TPM.txt",
skip_row_count = 0,
filter_expression = expression(TRUE),
dataset_id = "LungCancer1",
classification_criteria = "LUADVsControl",
classes = c("Control", "LUAD"),
cores = 16,
fems_to_run = c("ga_rf")),
#8
#LungCancer3 NSCLCVsCont
list(phenotype_file_name = "phenotype_info/phenotype_LungCancer3.txt",
read_count_dir_path = "data/LungCancer/3",
read_count_file_name = "GSE114711.txt",
skip_row_count = 0,
filter_expression = expression(TRUE),
dataset_id = "LungCancer3",
classification_criteria = "NSCLCVsCont",
classes = c("control", "NSCLC"),
cores = 16,
fems_to_run = c("ga_rf")),
#9
#LungCancer3 ENSCLCVsCont
list(phenotype_file_name = "phenotype_info/phenotype_LungCancer3.txt",
read_count_dir_path = "data/LungCancer/3",
read_count_file_name = "GSE114711.txt",
skip_row_count = 0,
filter_expression = expression(TRUE),
dataset_id = "LungCancer3",
classification_criteria = "ENSCLCVsCont",
classes = c("control", "earlystageNSCLC"),
cores = 16,
fems_to_run = c("ga_rf")),
#10
#LungCancer3 LNSCLCVsCont
list(phenotype_file_name = "phenotype_info/phenotype_LungCancer3.txt",
read_count_dir_path = "data/LungCancer/3",
read_count_file_name = "GSE114711.txt",
skip_row_count = 0,
filter_expression = expression(TRUE),
dataset_id = "LungCancer3",
classification_criteria = "LNSCLCVsCont",
classes = c("control", "latestageNSCLC"),
cores = 16,
fems_to_run = c("ga_rf")),
#11
#LungCancer3 LNSCLCVsENSCLC
list(phenotype_file_name = "phenotype_info/phenotype_LungCancer3.txt",
read_count_dir_path = "data/LungCancer/3",
read_count_file_name = "GSE114711.txt",
skip_row_count = 0,
filter_expression = expression(TRUE),
dataset_id = "LungCancer3",
classification_criteria = "LNSCLCVsENSCLC",
classes = c("earlystageNSCLC", "latestageNSCLC"),
cores = 16,
fems_to_run = c("ga_rf")),
#12
#TEP2015 GBMVsHC
list(phenotype_file_name = "phenotype_info/phenotype_TEP2015.txt",
read_count_dir_path = "data/GBM/TEP",
read_count_file_name = "GSE68086_TEP_data_matrix.txt",
skip_row_count = 0,
filter_expression = expression(TRUE),
dataset_id = "TEP2015",
classification_criteria = "GBMVsHC",
classes = c("HC", "GBM"),
cores = 16,
fems_to_run = c("ga_rf")),
#13
#TEP2015 NSCLCVsHC
list(phenotype_file_name = "phenotype_info/phenotype_TEP2015.txt",
read_count_dir_path = "data/GBM/TEP",
read_count_file_name = "GSE68086_TEP_data_matrix.txt",
skip_row_count = 0,
filter_expression = expression(TRUE),
dataset_id = "TEP2015",
classification_criteria = "NSCLCVsHC",
classes = c("HC", "NSCLC"),
cores = 16,
fems_to_run = c("ga_rf")),
#14
#TEP2015 CancerVsHC
list(phenotype_file_name = "phenotype_info/phenotype_TEP2015.txt",
read_count_dir_path = "data/GBM/TEP",
read_count_file_name = "GSE68086_TEP_data_matrix.txt",
skip_row_count = 0,
filter_expression = expression(TRUE),
dataset_id = "TEP2015",
classification_criteria = "CancerVsHC",
classes = c("HC", "Cancer"),
cores = 16,
fems_to_run = c("ga_rf")),
#15
#TEP2017 NSCLCVsNC
list(phenotype_file_name = "phenotype_info/phenotype_TEP2017.txt",
read_count_dir_path = "data/LungCancer/TEP",
read_count_file_name = "GSE89843_TEP_Count_Matrix.txt",
skip_row_count = 0,
filter_expression = expression(TRUE),
dataset_id = "TEP2017",
classification_criteria = "NSCLCVsNC",
classes = c("NonCancer", "NSCLC"),
cores = 32,
fems_to_run = c("ga_rf")),
#16
#TEP2015 CRCVsHC
list(phenotype_file_name = "phenotype_info/phenotype_TEP2015.txt",
read_count_dir_path = "data/GBM/TEP",
read_count_file_name = "GSE68086_TEP_data_matrix.txt",
skip_row_count = 0,
filter_expression = expression(TRUE),
dataset_id = "TEP2015",
classification_criteria = "CRCVsHC",
classes = c("HC", "CRC"),
cores = 16,
fems_to_run = c("ga_rf")),
#17
#TEP2015 BCsHC
list(phenotype_file_name = "phenotype_info/phenotype_TEP2015.txt",
read_count_dir_path = "data/GBM/TEP",
read_count_file_name = "GSE68086_TEP_data_matrix.txt",
skip_row_count = 0,
filter_expression = expression(TRUE),
dataset_id = "TEP2015",
classification_criteria = "BCVsHC",
classes = c("HC", "BC"),
cores = 16,
fems_to_run = c("ga_rf")),
#18
#TEP2015 PCsHC
list(phenotype_file_name = "phenotype_info/phenotype_TEP2015.txt",
read_count_dir_path = "data/GBM/TEP",
read_count_file_name = "GSE68086_TEP_data_matrix.txt",
skip_row_count = 0,
filter_expression = expression(TRUE),
dataset_id = "TEP2015",
classification_criteria = "PCVsHC",
classes = c("HC", "PancC"),
cores = 16,
fems_to_run = c("ga_rf")),
#19
#GSE71008 CRCVsHC
list(phenotype_file_name = "phenotype_info/phenotype_GSE71008.txt",
read_count_dir_path = "data/GSE71008",
read_count_file_name = "GSE71008_Data_matrix.txt",
skip_row_count = 0,
filter_expression = expression(TRUE),
dataset_id = "GSE71008",
classification_criteria = "CRCVsHC",
classes = c("HC", "CRC"),
cores = 16,
fems_to_run = c("ga_rf")),
#20
#GSE83270 BCVsHC
list(phenotype_file_name = "phenotype_info/phenotype_GSE83270.txt",
read_count_dir_path = "data/GSE83270",
read_count_file_name = "GSE83270_series_matrix.txt",
skip_row_count = 57,
row_count = 2158,
filter_expression = expression(TRUE),
dataset_id = "GSE83270",
classification_criteria = "BCVsHC",
classes = c("HC", "BC"),
cores = 16,
fems_to_run = c("ga_rf")),
#21
#GSE22981 EBCVsHC (Early Stage Breast Cancer Vs Healthy Control)
list(phenotype_file_name = "phenotype_info/phenotype_GSE22981.txt",
read_count_dir_path = "data/GSE22981",
read_count_file_name = "GSE22981_series_matrix.txt",
skip_row_count = 64,
row_count = 1145,
filter_expression = expression(TRUE),
dataset_id = "GSE22981",
classification_criteria = "EBCVsHC",
classes = c("HC", "EBC"),
cores = 16,
fems_to_run = c("ga_rf")),
#22
#GSE73002 BCVsNC
list(phenotype_file_name = "phenotype_info/phenotype_GSE73002.txt",
read_count_dir_path = "data/GSE73002",
read_count_file_name = "GSE73002_series_matrix.txt",
skip_row_count = 73,
row_count = 2540,
na_strings = "null",
filter_expression = expression(TRUE),
dataset_id = "GSE73002",
classification_criteria = "BCVsNC",
classes = c("NC", "BC"),
cores = 32,
fems_to_run = c("ga_rf")),
#23
#GSE44281 BCVsNC
list(phenotype_file_name = "phenotype_info/phenotype_GSE44281.txt",
read_count_dir_path = "data/GSE44281",
read_count_file_name = "GSE44281_series_matrix.txt",
skip_row_count = 67,
row_count = 20180,
filter_expression = expression(TRUE),
dataset_id = "GSE44281",
classification_criteria = "caseVsnoncase",
classes = c("noncase", "case"),
cores = 32,
fems_to_run = c("ga_rf")),
############
#RF_RFE executions
#1
#GBM1 GBMVsCont
#filter <- expression(Age > 55 & Sex == 'M')
list(phenotype_file_name = "phenotype_info/phenotype_GBM1.txt",
read_count_dir_path = "data/GBM/1",
read_count_file_name = "GSE122488_normalized_microRNA_counts.txt",
skip_row_count = 3,
filter_expression = expression(TRUE),
dataset_id = "GBM1",
classification_criteria = "GBMvsCont",
classes = c("Control", "GBM"),
cores = 16,
fems_to_run = c("RF_RFE")),
#2
#GBM1 GBMvsGlioma
list(phenotype_file_name = "phenotype_info/phenotype_GBM1.txt",
read_count_dir_path = "data/GBM/1",
read_count_file_name = "GSE122488_normalized_microRNA_counts.txt",
skip_row_count = 3,
filter_expression = expression(TRUE),
dataset_id = "GBM1",
classification_criteria = "GBMvsGlioma",
classes = c("Glioma", "GBM"),
cores = 16,
fems_to_run = c("RF_RFE")),
#3
#GBM1 GliomavsCont
list(phenotype_file_name = "phenotype_info/phenotype_GBM1.txt",
read_count_dir_path = "data/GBM/1",
read_count_file_name = "GSE122488_normalized_microRNA_counts.txt",
skip_row_count = 3,
filter_expression = expression(TRUE),
dataset_id = "GBM1",
classification_criteria = "GliomavsCont",
classes = c("Control", "Glioma"),
cores = 16,
fems_to_run = c("RF_RFE")),
#4
#GBM2 GBMVsNC
list(phenotype_file_name = "phenotype_info/phenotype_GBM2.txt",
read_count_dir_path = "data/GBM/2",
read_count_file_name = "GSE112462.txt",
skip_row_count = 0,
filter_expression = expression(TRUE),
dataset_id = "GBM2",
classification_criteria = "GBMVsNC",
classes = c("NonCancer", "GBM"),
cores = 16,
fems_to_run = c("RF_RFE")),
#5
#GBM2 GBMVsAstro_Oligo
list(phenotype_file_name = "phenotype_info/phenotype_GBM2.txt",
read_count_dir_path = "data/GBM/2",
read_count_file_name = "GSE112462.txt",
skip_row_count = 0,
filter_expression = expression(TRUE),
dataset_id = "GBM2",
classification_criteria = "GBMVsAstro_Oligo",
classes = c("Astro_Oligo", "GBM"),
cores = 16,
fems_to_run = c("RF_RFE")),
#6
#GBM2 Astro_OligoVsNC
list(phenotype_file_name = "phenotype_info/phenotype_GBM2.txt",
read_count_dir_path = "data/GBM/2",
read_count_file_name = "GSE112462.txt",
skip_row_count = 0,
filter_expression = expression(TRUE),
dataset_id = "GBM2",
classification_criteria = "Astro_OligoVsNC",
classes = c("NonCancer", "Astro_Oligo"),
cores = 16,
fems_to_run = c("RF_RFE")),
#7
#LungCancer1 LUADVsControl
list(phenotype_file_name = "phenotype_info/phenotype_LungCancer1.txt",
read_count_dir_path = "data/LungCancer/1",
read_count_file_name = "GSE111803_Readcount_TPM.txt",
skip_row_count = 0,
filter_expression = expression(TRUE),
dataset_id = "LungCancer1",
classification_criteria = "LUADVsControl",
classes = c("Control", "LUAD"),
cores = 16,
fems_to_run = c("RF_RFE")),
#8
#LungCancer3 NSCLCVsCont
list(phenotype_file_name = "phenotype_info/phenotype_LungCancer3.txt",
read_count_dir_path = "data/LungCancer/3",
read_count_file_name = "GSE114711.txt",
skip_row_count = 0,
filter_expression = expression(TRUE),
dataset_id = "LungCancer3",
classification_criteria = "NSCLCVsCont",
classes = c("control", "NSCLC"),
cores = 16,
fems_to_run = c("RF_RFE")),
#9
#LungCancer3 ENSCLCVsCont
list(phenotype_file_name = "phenotype_info/phenotype_LungCancer3.txt",
read_count_dir_path = "data/LungCancer/3",
read_count_file_name = "GSE114711.txt",
skip_row_count = 0,
filter_expression = expression(TRUE),
dataset_id = "LungCancer3",
classification_criteria = "ENSCLCVsCont",
classes = c("control", "earlystageNSCLC"),
cores = 16,
fems_to_run = c("RF_RFE")),
#10
#LungCancer3 LNSCLCVsCont
list(phenotype_file_name = "phenotype_info/phenotype_LungCancer3.txt",
read_count_dir_path = "data/LungCancer/3",
read_count_file_name = "GSE114711.txt",
skip_row_count = 0,
filter_expression = expression(TRUE),
dataset_id = "LungCancer3",
classification_criteria = "LNSCLCVsCont",
classes = c("control", "latestageNSCLC"),
cores = 16,
fems_to_run = c("RF_RFE")),
#11
#LungCancer3 LNSCLCVsENSCLC
list(phenotype_file_name = "phenotype_info/phenotype_LungCancer3.txt",
read_count_dir_path = "data/LungCancer/3",
read_count_file_name = "GSE114711.txt",
skip_row_count = 0,
filter_expression = expression(TRUE),
dataset_id = "LungCancer3",
classification_criteria = "LNSCLCVsENSCLC",
classes = c("earlystageNSCLC", "latestageNSCLC"),
cores = 16,
fems_to_run = c("RF_RFE")),
#12
#TEP2015 GBMVsHC
list(phenotype_file_name = "phenotype_info/phenotype_TEP2015.txt",
read_count_dir_path = "data/GBM/TEP",
read_count_file_name = "GSE68086_TEP_data_matrix.txt",
skip_row_count = 0,
filter_expression = expression(TRUE),
dataset_id = "TEP2015",
classification_criteria = "GBMVsHC",
classes = c("HC", "GBM"),
cores = 16,
fems_to_run = c("RF_RFE")),
#13
#TEP2015 NSCLCVsHC
list(phenotype_file_name = "phenotype_info/phenotype_TEP2015.txt",
read_count_dir_path = "data/GBM/TEP",
read_count_file_name = "GSE68086_TEP_data_matrix.txt",
skip_row_count = 0,
filter_expression = expression(TRUE),
dataset_id = "TEP2015",
classification_criteria = "NSCLCVsHC",
classes = c("HC", "NSCLC"),
cores = 16,
fems_to_run = c("RF_RFE")),
#14
#TEP2015 CancerVsHC
list(phenotype_file_name = "phenotype_info/phenotype_TEP2015.txt",
read_count_dir_path = "data/GBM/TEP",
read_count_file_name = "GSE68086_TEP_data_matrix.txt",
skip_row_count = 0,
filter_expression = expression(TRUE),
dataset_id = "TEP2015",
classification_criteria = "CancerVsHC",
classes = c("HC", "Cancer"),
cores = 16,
fems_to_run = c("RF_RFE")),
#15
#TEP2017 NSCLCVsNC
list(phenotype_file_name = "phenotype_info/phenotype_TEP2017.txt",
read_count_dir_path = "data/LungCancer/TEP",
read_count_file_name = "GSE89843_TEP_Count_Matrix.txt",
skip_row_count = 0,
filter_expression = expression(TRUE),
dataset_id = "TEP2017",
classification_criteria = "NSCLCVsNC",
classes = c("NonCancer", "NSCLC"),
cores = 32,
fems_to_run = c("RF_RFE")),
#16
#TEP2015 CRCVsHC
list(phenotype_file_name = "phenotype_info/phenotype_TEP2015.txt",
read_count_dir_path = "data/GBM/TEP",
read_count_file_name = "GSE68086_TEP_data_matrix.txt",
skip_row_count = 0,
filter_expression = expression(TRUE),
dataset_id = "TEP2015",
classification_criteria = "CRCVsHC",
classes = c("HC", "CRC"),
cores = 16,
fems_to_run = c("RF_RFE")),
#17
#TEP2015 BCsHC
list(phenotype_file_name = "phenotype_info/phenotype_TEP2015.txt",
read_count_dir_path = "data/GBM/TEP",
read_count_file_name = "GSE68086_TEP_data_matrix.txt",
skip_row_count = 0,
filter_expression = expression(TRUE),
dataset_id = "TEP2015",
classification_criteria = "BCVsHC",
classes = c("HC", "BC"),
cores = 16,
fems_to_run = c("RF_RFE")),
#18
#TEP2015 PCsHC
list(phenotype_file_name = "phenotype_info/phenotype_TEP2015.txt",
read_count_dir_path = "data/GBM/TEP",
read_count_file_name = "GSE68086_TEP_data_matrix.txt",
skip_row_count = 0,
filter_expression = expression(TRUE),
dataset_id = "TEP2015",
classification_criteria = "PCVsHC",
classes = c("HC", "PancC"),
cores = 16,
fems_to_run = c("RF_RFE")),
#19
#GSE71008 CRCVsHC
list(phenotype_file_name = "phenotype_info/phenotype_GSE71008.txt",
read_count_dir_path = "data/GSE71008",
read_count_file_name = "GSE71008_Data_matrix.txt",
skip_row_count = 0,
filter_expression = expression(TRUE),
dataset_id = "GSE71008",
classification_criteria = "CRCVsHC",
classes = c("HC", "CRC"),
cores = 16,
fems_to_run = c("RF_RFE")),
#20
#GSE83270 BCVsHC
list(phenotype_file_name = "phenotype_info/phenotype_GSE83270.txt",
read_count_dir_path = "data/GSE83270",
read_count_file_name = "GSE83270_series_matrix.txt",
skip_row_count = 57,
row_count = 2158,
filter_expression = expression(TRUE),
dataset_id = "GSE83270",
classification_criteria = "BCVsHC",
classes = c("HC", "BC"),
cores = 16,
fems_to_run = c("RF_RFE")),
#21
#GSE22981 EBCVsHC (Early Stage Breast Cancer Vs Healthy Control)
list(phenotype_file_name = "phenotype_info/phenotype_GSE22981.txt",
read_count_dir_path = "data/GSE22981",
read_count_file_name = "GSE22981_series_matrix.txt",
skip_row_count = 64,
row_count = 1145,
filter_expression = expression(TRUE),
dataset_id = "GSE22981",
classification_criteria = "EBCVsHC",
classes = c("HC", "EBC"),
cores = 16,
fems_to_run = c("RF_RFE")),
#22
#GSE73002 BCVsNC
list(phenotype_file_name = "phenotype_info/phenotype_GSE73002.txt",
read_count_dir_path = "data/GSE73002",
read_count_file_name = "GSE73002_series_matrix.txt",
skip_row_count = 73,
row_count = 2540,
na_strings = "null",
filter_expression = expression(TRUE),
dataset_id = "GSE73002",