xina_analysis: xina_analysis

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

Description

xina_analysis is to analyze protein-protein interaction(PPI) networks using STRINGdb and igraph R package. This module computes PPI networks within each XINA clusters.

Usage

xina_analysis(clustering_result, ppi_db, is_stringdb = TRUE,
  flag_simplify = TRUE, node_shape = "sphere",
  num_clusters_in_row = 5, img_size = NULL, img_qual = 300)

Arguments

clustering_result	A list containing XINA clustering results. See xina_clustering
ppi_db	STRINGdb object
is_stringdb	If it is TRUE (default), XINA will process 'ppi_db' as STRINGdb, but it is FALSE, XINA will accepts your 'ppi_db' as it is. You can make your own igraph network using customized PPI information instead of STRINGdb.
flag_simplify	If it is TRUE (default), XINA will exclude unconnected proteins
node_shape	You can choose node shape. Default is "sphere". See shapes
num_clusters_in_row	The number of clusters in a row on the XINA network plot. Default is 5.
img_size	Set the image size. For width=1000 and height=1500, it is img_size=c(1000,1500).
img_qual	Set the image resolution. Default is 300.

Value

A PNG file (XINA_Cluster_Networks.png) displaying PPI network plots of all the clusters and a list containing XINA network analysis results.

Item	Description
All_network	PPI network of all the input proteins
Sub_network	A list containing PPI networks of each clusters
Data	XINA clustering results. See xina_clustering
Nodes	A list of proteins in each cluster
Conditions	A list of experimental condition of proteins in each cluster
Titles	A list of plot titles for XINA plotting
out_dir	A directory path storing XINA network analysis results
is_stringdb	False = different PPI DB and TRUE = STRING DB

Examples

## Not run: 
# load XINA example data
data(xina_example)

# use the following code for utilizing up-to-date STRING DB
tax_id <- 9606  # for human
# tax_id <- 10090  # for mouse
library(STRINGdb)
library(igraph)
string_db <- STRINGdb$new( version='10', species=tax_id, score_threshold=0, input_directory='' )
string_db
xina_result <- xina_analysis(example_clusters, string_db, flag_simplify=FALSE)

# Run XINA with a protein-protein interaction edgelist
data(HPRD)
net_all <- simplify(graph_from_data_frame(d=hprd_ppi, directed=FALSE),
remove.multiple = FALSE, remove.loops = TRUE)
xina_result <- xina_analysis(example_clusters, net_all, is_stringdb=FALSE, flag_simplify=FALSE)

## End(Not run)

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