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
-
-d,--data<data>¶ Required Name of the cancer dataset from TCGA
- Options
prad | ov | kirc | brca | lihc
-
-p,--permutations<permutations>¶ Number of permutations
- Default
100
ora¶
Perform ORA analysis.
pathway_forte ora [OPTIONS] COMMAND [ARGS]...
hypergeometric¶
Perform one-tailed hypergeometric test enrichment.
pathway_forte ora hypergeometric [OPTIONS]
Options
-
-d,--genesets<genesets>¶ Required Path to GMT file
-
-s,--fold-changes<fold_changes>¶ Required Path to fold changes file
-
--no-threshold¶ Do not apply threshold
-
-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>¶ Required Name of the cancer dataset from TCGA
- Options
prad | ov | kirc | brca | lihc
-
--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
subtype¶
Train subtype analysis.
pathway_forte prediction subtype [OPTIONS]
Options
-
-d,--ssgsea<ssgsea>¶ Required Path to ssGSEA file
-
-s,--subtypes<subtypes>¶ Required Path to the subtypes file
-
--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
-
--chain-pca¶
-
--explained-variance<explained_variance>¶ Explained variance
- Default
0.95
-
--turn-off-warnings¶ Turns off warnings
survival¶
Train survival model.
pathway_forte prediction survival [OPTIONS]
Options
-
-d,--data<data>¶ Required Name of dataset
-
--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¶
Test stability of prediction.
pathway_forte prediction test-stability-prediction [OPTIONS]
Options
-
-s,--ssgsea-scores-path<ssgsea_scores_path>¶ Required ssGSEA scores file
-
-p,--phenotypes-path<phenotypes_path>¶ Required Path to the phenotypes file
-
--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