Command Line Interface¶
PathwayForte commands.
pathway_forte¶
Run PathwayForte.
pathway_forte [OPTIONS] COMMAND [ARGS]...
fcs¶
List of FCS Analyses.
pathway_forte fcs [OPTIONS] COMMAND [ARGS]...
gsea¶
Run GSEA on TCGA data.
pathway_forte fcs gsea [OPTIONS]
Options
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-d,--data<data>¶ Name of the cancer dataset from TCGA [required]
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-p,--permutations<permutations>¶ Number of permutations [default: 100]
ora¶
Perform ORA analysis.
pathway_forte ora [OPTIONS] COMMAND [ARGS]...
hypergeometric¶
Performs one-tailed hypergeometric test enrichment.
pathway_forte ora hypergeometric [OPTIONS]
Options
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-d,--genesets<genesets>¶ Path to GMT file [required]
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-s,--fold-changes<fold_changes>¶ Path to fold changes file [required]
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--no-threshold¶ Do not apply threshold
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-o,--output<output>¶ Optional path for output JSON file
prediction¶
List of Prediction Methods.
pathway_forte prediction [OPTIONS] COMMAND [ARGS]...
binary¶
Train elastic net for binary prediction.
pathway_forte prediction binary [OPTIONS]
Options
-
-d,--data<data>¶ Name of the cancer dataset from TCGA [required]
-
--outer-cv<outer_cv>¶ Number of splits in outer cross-validation [default: 10]
-
--inner-cv<inner_cv>¶ Number of splits in inner cross-validation [default: 10]
-
-i,--max_iterations<max_iterations>¶ Number of max iterations to converge [default: 1000]
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--turn-off-warnings¶ Turns off warnings
subtype¶
Train subtype analysis.
pathway_forte prediction subtype [OPTIONS]
Options
-
-d,--ssgsea<ssgsea>¶ Path to ssGSEA file [required]
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-s,--subtypes<subtypes>¶ Path to the subtypes file [required]
-
--outer-cv<outer_cv>¶ Number of splits in outer cross-validation [default: 10]
-
--inner-cv<inner_cv>¶ Number of splits in inner cross-validation [default: 10]
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--chain-pca¶
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--explained-variance<explained_variance>¶ Explained variance [default: 0.95]
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--turn-off-warnings¶ Turns off warnings
survival¶
Train survival model.
pathway_forte prediction survival [OPTIONS]
Options
-
-d,--data<data>¶ Name of dataset [required]
-
--outer-cv<outer_cv>¶ Number of splits in outer cross-validation [default: 10]
-
--inner-cv<inner_cv>¶ Number of splits in inner cross-validation [default: 10]
-
--turn-off-warnings¶ Turns off warnings
test-stability-prediction¶
pathway_forte prediction test-stability-prediction [OPTIONS]
Options
-
-s,--ssgsea-scores-path<ssgsea_scores_path>¶ ssGSEA scores file [required]
-
-p,--phenotypes-path<phenotypes_path>¶ Path to the phenotypes file [required]
-
--outer-cv<outer_cv>¶ Number of splits in outer cross-validation [default: 10]
-
--inner-cv<inner_cv>¶ Number of splits in inner cross-validation [default: 10]
-
-i,--max_iterations<max_iterations>¶ Number of max iterations to converge [default: 1000]
-
--turn-off-warnings¶ Turns off warnings