Combine 2 pathfindR Results

combine_pathfindR_results(result_A, result_B, plot_common = TRUE)

## Arguments

result_A data frame of first pathfindR enrichment results data frame of second pathfindR enrichment results boolean to indicate whether or not to plot the term-gene graph of the common terms (default=TRUE)

## Value

Data frame of combined pathfindR enrichment results. Columns are:

ID

ID of the enriched term

Term_Description

Description of the enriched term

Fold_Enrichment_A

Fold enrichment value for the enriched term (Calculated using ONLY the input genes)

occurrence_A

the number of iterations that the given term was found to enriched over all iterations

lowest_p_A

the lowest adjusted-p value of the given term over all iterations

highest_p_A

the highest adjusted-p value of the given term over all iterations

Up_regulated_A

the up-regulated genes in the input involved in the given term's gene set, comma-separated

Down_regulated_A

the down-regulated genes in the input involved in the given term's gene set, comma-separated

Fold_Enrichment_B

Fold enrichment value for the enriched term (Calculated using ONLY the input genes)

occurrence_B

the number of iterations that the given term was found to enriched over all iterations

lowest_p_B

the lowest adjusted-p value of the given term over all iterations

highest_p_B

the highest adjusted-p value of the given term over all iterations

Up_regulated_B

the up-regulated genes in the input involved in the given term's gene set, comma-separated

Down_regulated_B

the down-regulated genes in the input involved in the given term's gene set, comma-separated

combined_p

the combined p value (via Fisher's method)

status

whether the term is found in both analyses ("common"), found only in the first ("A only") or found only in the second ("B only)

By default, the function also displays the term-gene graph of the common terms

## Examples

combined_results <- combine_pathfindR_results(RA_output, RA_comparison_output)
#> Warning: ggrepel: 1 unlabeled data points (too many overlaps). Consider increasing max.overlaps
#> You may run combined_results_graph() to create visualizations of combined term-gene graphs of selected terms