enrichfind_hp: Functional Enrichment Analysis of all Host Proteins

In mrbakhsh/HPiP: Host-Pathogen Interaction Prediction

Functional Enrichment Analysis of all Host Proteins

Description

This function uses gost function in gprofiler2 package to perfrom functional enrichment analysis for all predicted host proteins in the high-confidence network.

Usage

enrichfind_hp(
  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

enrichfind_hp

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 <- enrichfind_hp(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.