xina_analysis {XINA} | R Documentation

## xina_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)

[Package XINA version 1.0.1 Index]