enrichfindP {HPiP} | R Documentation |
This function uses gost
function
in gprofiler2
package to perfrom functional enrichment analysis
for pathogen interactors in the high-confidence network.
enrichfindP( ppi, threshold = 0.05, sources = c("GO", "KEGG"), p.corrction.method = "bonferroni", org = "hsapiens" )
ppi |
A data.frame containing pathogen proteins in the first column and host proteins in the second column. |
threshold |
Custom p-value threshold for significance. |
sources |
A vector of data sources to use.
See |
p.corrction.method |
The algorithm used for multiple testing
correction;defaults to 'bonferroni'.
See |
org |
An organism name;defaults to 'hsapiens'.
See |
enrichfindP
A data.frame with the enrichment analysis results.
Matineh Rahmatbakhsh, matinerb.94@gmail.com
See enrichplot
for plotting enrichment analysis.
data('predicted_PPIs') #perform enrichment enrich.df <- enrichfindP(predicted_PPIs, threshold = 0.05, sources = c("GO", "KEGG"), p.corrction.method = "bonferroni", org = "hsapiens")