SiGN-Proc is a CUI-based (command line) tool to process gene network files, including converting file formats, extracting subnetworks, coloring the specified nodes, and so on.
In SiGN-Proc, you specify filters to process networks. Many filters are available in SiGN-Proc. One filter reads a network from a file. One extracts a sub network. You can specify multiple filters. In such a case, a network processed by a filter is passed to the next filter.
Note: This document is currently under development.
--help
Show help message.
Here are some examples. Specify the following as filters above when you execute SiGN-Proc.
This example converts the network file network.sgn3 written in the SGN3 format into the CSML format file network.csml. See File Formats for details of the available file formats.
This extracts IL6 and its parents and children from network.csml.
The filter can be specified by --filter_name followed by its key=value style arguments concatenated by commas. White spaces can be inserted after the camma.
Execute "signproc --help filter" for the full list of available filters, and "signproc --help filter,filter_name" for the detailed description of filter_name.
This removes all edges except for ones whose properties specified by name satisfy the condition specified by op and value.
name=property_name
type=property_type
op= { eq | ge | gt | le | lt }
value= value
noprop= { stop | remove | ignore }
This removes edges whose bootstrap probabilities are less than or equal to 0.5.
This leaves edges that are estimated as up-regulated ones.
This filter reads a network, data frame, or dataset from a file, and then passes it to the next filter.
type= { edf | frame | network_format }
file= file_name
The subnet filter extracts a sub network based on a node names given by a file or a list of node names.
file=file_name
col=n
node=node1:node2:...
dist=n
Output a network into a file. This passes the received network to the next filter without modifying or processing it. Therefore, by using multiple output filters, users can output a network in files in various formats.
file=file_name
type=network_format
args=\{key1=value1,...\}
The BS filter is to compile the bootstrapped networks into a single network.
prefix=file_name_prefix
dynamic
ed=n
bg=n
th=threahold
ver=n
file=file_name
col=n
color=r:g:b [:a ]
The Comp filter is to compare two network structures. This filter does not change the network. Instead, it compares the network with another one specified by the arguments. After the comparison, it prints the comparison result. This regards the network given by the arguments as a true network of the demanded one and counts the number of true positive (TP), false positive (FP), true negative (TN) and false negative (FN) edges of the network passed by SiGN-Proc.
The TP edges are ones that exist in the both network. The FP edges are ones that exist only in the original network passwd by SiGN-Proc. The FN edges are ones that exist only in the true network given by the arguments.
The TP, FP, FN edges can be saved as separate network files by specifying the tp, fp, and fn arguments.
file=file_name
type=file_type
args=\{key1=value1,...\}
tp=file_name
tptype=file_type
tpargs=\{key1=value1,...\}
fp=file_name
fptype=file_type
fpargs=\{key1=value1,...\}
fn=file_name
fntype=file_type
fnargs=\{key1=value1,...\}
The score filter calculates the network score. This filter does not change the network structure at all. This prints the calculated score to the standard output.
data=file_name
score_args=\{key1=value1,...\}
dynamic
mem=memory_size
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Contact: Yoshinori Tamada <tamada ATMARK ytlab.jp>