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