enrichfindP: Functional Enrichment Analysis for Pathogen Interactors in...

In mrbakhsh/HPiP: Host-Pathogen Interaction Prediction

Functional Enrichment Analysis for Pathogen Interactors in the High-Confidence Network.

Description

This function uses gost function in gprofiler2 package to perfrom functional enrichment analysis for pathogen interactors in the high-confidence network.

Usage

enrichfindP(
  ppi,
  threshold = 0.05,
  sources = c("GO", "KEGG"),
  p.corrction.method = "bonferroni",
  org = "hsapiens"
)

Arguments

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 gost for more details.
p.corrction.method	The algorithm used for multiple testing correction;defaults to 'bonferroni'. See gost for more details.
org	An organism name;defaults to 'hsapiens'. See gost for more details.

Details

enrichfindP

Value

A data.frame with the enrichment analysis results.

Author(s)

Matineh Rahmatbakhsh, [e-mail]

See Also

See enrichplot for plotting enrichment analysis.

Examples

data('predicted_PPIs')
#perform enrichment
enrich.df <- enrichfindP(predicted_PPIs,
threshold = 0.05,
sources = c("GO", "KEGG"),
p.corrction.method = "bonferroni",
org = "hsapiens")

mrbakhsh/HPiP documentation built on March 28, 2023, 4:35 p.m.