xina_enrichment: xina_enrichment

In langholee/XINA: Multiplexes Isobaric Mass Tagged-based Kinetics Data for Network Analysis

Description

xina_enrichment conducts functional enrichment tests using gene ontology or KEGG pathway terms for a given protein list

Usage

xina_enrichment(string_db, protein_list, enrichment_type = "GO",
  pval_threshold = 0.05, methodMT = "fdr")

Arguments

string_db	STRINGdb object
protein_list	A vector of gene names to draw protein-protein interaction network.
enrichment_type	A functional annotation for the enrichment test. 'enrichment_type' should be one of 'GO' and 'KEGG',
pval_threshold	P-value threshold to get significantly enriched terms from the given proteins
methodMT	Method for p-value adjustment. See get_enrichment. Default is 'fdr'.

Value

A list of data frames containing enrichment results

Examples

## Not run: 
library(STRINGdb)
library(Biobase)

# load XINA example data
data(xina_example)

# Get STRING database for protein-protein intereaction information
string_db <- STRINGdb$new( version="10", species=9606, score_threshold=0, input_directory="" )
string_db

# XINA analysis with STRING DB
xina_result <- xina_analysis(example_clusters, string_db)

# Select proteins that showed cluster #1 in the Stimulus2 condition
subgroup <- subset(example_clusters$aligned, Stimulus2==1)
protein_list <- as.vector(subgroup$`Gene name`)

# Enrichment test using KEGG pathway terms that have adjuseted p-value less than 0.1
kegg_enriched <- xina_enrichment(string_db, protein_list,
enrichment_type = "KEGG", pval_threshold=0.1)
plot_enrichment_results(kegg_enriched$KEGG, num_terms=10)

# Enrichment test using GO terms that have adjuseted p-value less than 0.1
go_enriched <- xina_enrichment(string_db, protein_list,
enrichment_type = "GO", pval_threshold=0.1)
plot_enrichment_results(go_enriched$Component, num_terms=10)

## End(Not run)

langholee/XINA documentation built on March 17, 2020, 5:23 p.m.