example_pathfindR_output: Example Output for the pathfindR Enrichment Workflow -...
In pathfindR.data: Data Package for 'pathfindR'
example_pathfindR_output R Documentation
Example Output for the pathfindR Enrichment Workflow - Rheumatoid Arthritis
Description
The data frame containing the results of pathfindR's active-subnetwork-oriented
enrichment workflow performed on the rheumatoid arthritis
differential-expression data frame example_pathfindR_input. Analysis via
run_pathfindR was performed using the default settings.
Generated on Dec 11, 2022.
Usage
example_pathfindR_output
Format
A data frame with 128 rows and 9 columns:
- ID
ID of the enriched term
- Term_Description
Description of the enriched term
- Fold_Enrichment
Fold enrichment value for the enriched term
- occurrence
the number of iterations that the given term was found to enriched over all iterations
- support
the median support (proportion of active subnetworks leading to enrichment within an iteration) over all iterations
- lowest_p
the lowest adjusted-p value of the given term over all iterations
- highest_p
the highest adjusted-p value of the given term over all iterations
- Up_regulated
the up-regulated genes in the input involved in the given term, comma-separated
- Down_regulated
the down-regulated genes in the input involved in the given term, comma-separated
See Also
example_pathfindR_input for the RA differentially-expressed genes data frame
example_pathfindR_output_clustered for the RA example pathfindR clustering outputs
example_experiment_matrix for the RA differentially-expressed genes expression matrix
run_pathfindR for details on the pathfindR enrichment analysis
pathfindR.data documentation built on April 27, 2023, 9:07 a.m.
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| example_pathfindR_output | R Documentation |
Example Output for the pathfindR Enrichment Workflow - Rheumatoid Arthritis
Description
The data frame containing the results of pathfindR's active-subnetwork-oriented
enrichment workflow performed on the rheumatoid arthritis
differential-expression data frame example_pathfindR_input. Analysis via
run_pathfindR was performed using the default settings.
Generated on Dec 11, 2022.
Usage
example_pathfindR_output
Format
A data frame with 128 rows and 9 columns:
- ID
ID of the enriched term
- Term_Description
Description of the enriched term
- Fold_Enrichment
Fold enrichment value for the enriched term
- occurrence
the number of iterations that the given term was found to enriched over all iterations
- support
the median support (proportion of active subnetworks leading to enrichment within an iteration) over all iterations
- lowest_p
the lowest adjusted-p value of the given term over all iterations
- highest_p
the highest adjusted-p value of the given term over all iterations
- Up_regulated
the up-regulated genes in the input involved in the given term, comma-separated
- Down_regulated
the down-regulated genes in the input involved in the given term, comma-separated
See Also
example_pathfindR_input for the RA differentially-expressed genes data frame
example_pathfindR_output_clustered for the RA example pathfindR clustering outputs
example_experiment_matrix for the RA differentially-expressed genes expression matrix
run_pathfindR for details on the pathfindR enrichment analysis
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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