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params.yml
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params.yml
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######PIPELINE########
manifest: manifest.csv # <string>: Absolute path to manifest.csv
outDir: "output/outdir_all" # <string>: Absolute path to output directory
reportsDir: "output/reports_all" # <string>: Absolute path to reports directory
workDir: "output/workdir_all" # <string>: Absolute path to workdir directory
launchDir: "./" # <string>: Absolute path to launchdir directory
maxRetries: 2 # <integer>: Number of tries for processing
errorStrategy: retry # <string>: terminate/ignore/retry
####SPECTRAL PROCESSING####
check_pulse_samples: cpmgpr1d # <string>: pulse program from given manifest e.g. cpmgpr1d, noesy1d
rm_duplicated_names: false # <boolean>: true/false enable/disable removing duplicated sample names
lambda_bc: 5000000 # <integer>: Baseline correction lambda parameter, controlling smoothness of baseline
p_bc: 0.00001 # <float>: Baseline correction p_bc parameter, controlling stickiness of baseline
reverse_axis_samples: selected # <string>: selected/all reverse axis for either all samples or selected by automatic threshold
run_bucketing: true # <boolean>: true/ false enable/disable bucketing for simplify density of peaks before metabolites quantification
intmeth: t # <string>: Type of bucketing, rectangular or trapezoidal: one of r, t
mb: 15000 # <integer>: Number of buckets, default values supposed to be bigger than 5000 mb
run_warping: true # <boolean>: true/ false enable/disable warping for spectra re-aligning based on a reference spectrum
type_norm: pqn # <string>: Normalization type, one of: "mean", "pqn", "median", "firstquartile", "peak", default is pqn
removal_regions: list(Water = c(4.5, 5.1), Noise = c(0.0, 0.1)) # <string>: Regions from spectra to be removed, by default Water and Noise around 0 ppms. default "list(Water = c(4.5, 5.1), Noise = c(0.0, 0.1))"
ncores: 3 # <integer>: allocate number of threads for ASICS metabolites quantification task
quantif_method: both # <string>: Metabolites quantification method one of: FWER, Lasso, or both. default = "both"
####DATA ANALYSIS####
run_combine_project_batches: true # <boolean>: true/ false enable/disable merging datasets for data analysis where batch is not "None"
run_batch_correction: false # <boolean>: true/ false enable/disable ComBat batch correction
log1p: true # <boolean>: true/false enable/disable log1p normalization of metabolites before data analysis
metadata_column: Disease # <string>: column with binary state for data analysis module eg. "disease_state", "gender"
zeronan_threshold: 0.7 # <float>: Threshold for zero or NaN values in multivariate analysis, values from range 0-1
test_size: 0.3 # <integer>: Test size for splitting data in multivariate analysis, default = 30%
cross_val_fold: 2 # <float>: Cross-validation folds fo Logistic regression CV model, default = 2
pvalue_shapiro: 0.08 # <float>: (Optional). P-value threshold for normality Shapiro-Wilk test. default = 0.05
####BIOLOGICAL INTERPRETATION####
top_n: 3 # <intiger>: Number of metabolites to include in enrichment for pathway analysis, default = 20
kegg_org_id: pae # <string>: KEGG organism ID, default is human "hsa"