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config.yml
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139 lines (137 loc) · 5.92 KB
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mae_hdf5_prefix: "mae"
readable_names:
"Lipidomics, positive | transformed": "Lipidomics Set 1 (P)"
"Lipidomics, negative | transformed": "Lipidomics Set 1 (N)"
"Lipidomics-SPLINE | positive": "Lipidomics Set 2"
"Very long chain fatty acids | batch-adjusted": "VLCFA"
"Very long chain fatty acids": "VLCFA"
"Acylcarnitines | batch-adjusted | imputed missing values": "Acylcarnitines"
"Amino acids | batch-adjusted | imputed missing values": "Amino acids"
"Amino acids": "Amino acids"
"Acylcarnitines": "Acylcarnitines"
"Proteomics | imputed missing values": "Proteomics"
"Proteomics | with missing values": "Proteomics"
"Proteomics-IPP": "Proteomics-IPP"
"mRNA-seq-2 | batch-adjusted | corrected": "mRNA-seq"
"miRNA-seq, mature | batch-adjusted | cell-type adjusted": "miRNA-seq"
"miRNA-seq, mature | batch-adjusted": "miRNA-seq"
"miRNA qRT-PCR": "miRNA qRT-PCR"
"EM-seq | cell-type adjusted | 100,000 most variable CpG sites": "EM-seq (var)"
"EM-seq | cell-type adjusted | 100,000 random CpG sites": "EM-seq (random)"
"Metabolomics": "Metabolomics"
experiment_names:
PCA:
- "Lipidomics, positive | transformed"
- "Lipidomics, negative | transformed"
- "Lipidomics-SPLINE | positive"
- "Very long chain fatty acids | batch-adjusted"
- "Acylcarnitines | batch-adjusted | imputed missing values"
- "Amino acids | batch-adjusted | imputed missing values"
- "Proteomics | imputed missing values"
- "Proteomics-IPP"
- "mRNA-seq-2 | batch-adjusted | corrected"
- "miRNA-seq, mature | batch-adjusted | cell-type adjusted"
- "miRNA qRT-PCR"
- "EM-seq | cell-type adjusted | 100,000 most variable CpG sites"
RLM:
- "Lipidomics, positive | transformed"
- "Lipidomics, negative | transformed"
- "Lipidomics-SPLINE | positive"
- "Very long chain fatty acids | batch-adjusted"
# - "Very long chain fatty acids | unscaled"
- "Acylcarnitines | batch-adjusted | imputed missing values"
- "Amino acids | batch-adjusted | imputed missing values"
- "Proteomics-IPP"
- "Proteomics | imputed missing values"
# - "mRNA-seq-2 | batch-adjusted | corrected"
# - "miRNA-seq, mature | batch-adjusted | cell-type adjusted"
# - "miRNA qRT-PCR"
# - "EM-seq | cell-type adjusted | 100,000 most variable CpG sites"
MOFA:
- "Lipidomics, positive | transformed"
- "Very long chain fatty acids | batch-adjusted"
- "Acylcarnitines | batch-adjusted | imputed missing values"
- "Amino acids | batch-adjusted | imputed missing values"
# - "Proteomics | imputed missing values"
# - "Proteomics-IPP"
# - "mRNA-seq-2 | batch-adjusted | corrected"
# - "miRNA-seq, mature | batch-adjusted | cell-type adjusted"
# - "miRNA qRT-PCR"
# - "EM-seq | cell-type adjusted | 100,000 most variable CpG sites"
CV:
- "Lipidomics, positive | transformed"
- "Lipidomics, negative | transformed"
- "Lipidomics-SPLINE | positive"
- "Very long chain fatty acids"
- "Acylcarnitines"
- "Amino acids"
- "Proteomics | with missing values"
- "Proteomics-IPP"
- "mRNA-seq-2 | batch-adjusted | corrected"
- "miRNA-seq, mature | batch-adjusted | cell-type adjusted"
- "miRNA qRT-PCR"
- "EM-seq | cell-type adjusted | 100,000 most variable CpG sites"
# - "EM-seq | cell-type adjusted | 100,000 random CpG sites"
DIABLO:
- "Lipidomics, positive | transformed"
# - "Lipidomics, negative | transformed"
- "Lipidomics-SPLINE | positive"
- "Very long chain fatty acids | batch-adjusted"
- "Acylcarnitines | batch-adjusted | imputed missing values"
- "Amino acids | batch-adjusted | imputed missing values"
- "Proteomics | imputed missing values"
- "Proteomics-IPP"
- "mRNA-seq-2 | batch-adjusted | corrected"
- "miRNA-seq, mature | batch-adjusted | cell-type adjusted"
- "miRNA qRT-PCR"
- "EM-seq | cell-type adjusted | 100,000 most variable CpG sites"
# - "EM-seq | cell-type adjusted | 100,000 random CpG sites"
output_directory:
PCA: "Output/PCA"
RLM: "Output/RLM"
MOFA: "Output/MOFA"
DIABLO: "Output/DIABLO"
PEA: "Output/PEA"
CV: "Output/CV"
sample_selection:
include_MALE: TRUE
include_FEMALE: TRUE
additional_data_types:
include_hematology: FALSE
include_phenotype: FALSE
num_MOFA_factors: 12
PEA_input:
DIABLO:
"Lipidomics, positive": "DIABLO/XYloadings_Lipidomics__positive.csv"
"Lipidomics, negative": "DIABLO/XYloadings_Lipidomics__negative.csv"
"Very long chain fatty acids | batch-adjusted": "DIABLO/XYloadings_Very_long_chain_fatty_acids___batch-adjusted.csv"
"Acylcarnitines | batch-adjusted | imputed missing values": "DIABLO/XYloadings_Acylcarnitines___batch-adjusted___imputed_missing_values.csv"
"Amino acids | batch-adjusted | imputed missing values": "DIABLO/XYloadings_Amino_acids___batch-adjusted___imputed_missing_values.csv"
"Proteomics | imputed missing values": "DIABLO/XYloadings_Proteomics___imputed_missing_values.csv"
MOFA:
#"Lipidomics, positive": "MOFA/factorweights_Lipidomics__positive___transformed.csv"
"Very long chain fatty acids | batch-adjusted": "MOFA/factorweights_Very_long_chain_fatty_acids___batch-adjusted.csv"
"Acylcarnitines | batch-adjusted | imputed missing values": "MOFA/factorweights_Acylcarnitines___batch-adjusted___imputed_missing_values.csv"
"Amino acids | batch-adjusted | imputed missing values": "MOFA/factorweights_Amino_acids___batch-adjusted___imputed_missing_values.csv"
"Proteomics | imputed missing values": "MOFA/factorweights_Proteomics___imputed_missing_values.csv"
"Proteomics-IPP": "MOFA/factorweights_Proteomics-IPP.csv"
"mRNA-seq-2 | batch-adjusted | corrected": "MOFA/factorweights_mRNA-seq-2___batch-adjusted___vst___corrected.csv"
#"EM-seq | cell-type adjusted | 100,000 most variable CpG sites": "MOFA/factorweights_EM-seq___cell-type_adjusted___100_000_most_variable_CpG_sites.csv"
PEA_databases: "all"
PEA_rankings:
DIABLO:
- "comp1"
- "comp2"
MOFA:
- "Factor1"
- "Factor2"
- "Factor3"
- "Factor4"
- "Factor5"
- "Factor6"
- "Factor7"
- "Factor8"
- "Factor9"
- "Factor10"
- "Factor11"
- "Factor12"