Module: RJE_PPI Description: RJE Protein-Protein Interaction Module Version: 2.9.0 Last Edit: 14/05/19

Copyright © 2010 Richard J. Edwards - See source code for GNU License Notice

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Imported modules: rje rje_db rje_svg rje_xgmml rje_zen

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See SLiMSuite Blog for further documentation. See rje for general commands.

Function

This module is contains methods for manipulating protein-protein interaction (PPI) dictionaries. Database-specific classes and methods can be found in rje_hprd and rje_biogrid, while broader-scale functionality is found in the PINGU application. With time, generic PINGU functions should be migrated to this module and used by PINGU.

The main purpose of rje_ppi is for use within other applications but there is also some standalone functionality for reading in a pairwise PPI file of delimited data with "Hub", "Spoke" and "Evidence" columns.

Data is stored as an unannotated graph {Hub:[Spokes]} or an annotated graph {Hub:{Spoke:Evidence}} and rje_db Database tables that store additional Node and Edge data. Edge data is read directly from PPI Pairwise input, with 'Hub' and 'Edge' fields that combine to make the key. The Edge table will have an "Evidence" field and optional additional fields. The Node table will have a 'Node' field as the key (that matches the 'Hub' or 'Spoke' from the Edge table).

Commandline

Input Options

pairwise=FILE : Input PPI pairwise file, containing Hub, Spoke and optional Evidence columns []
nodelist=LIST : Reduce input PPI to given Node list []
nodemap=X : Try to map Nodes first using Node table field X []
expandppi=X : Expand reduced Node list by X PPI levels [0]
combineppi=LIST : List of pairwise PPI files (using same ID set) to import. Uses Evidence field or filename []
nodefields=LIST : List of alternative A/B fields to replace Hub and Spoke fields [SYMBOL_,Gene_]
ppisym=T/F : Whether to enforce Hub/Spoke symmetry [True]

Output/Processing Options

ppiout=FILE : Save pairwise PPI file following processing (if rest=None) (T=basefile.pairwise.tdt) [None]
tabout=T/F : Output PPI data as Node and Edge tables [False]
fragment=T/F : Perform PPI fragmentation [False]
fragsize=X : Combine smaller fragments upto fragsize [200]
minfrag=X : Minimum fragment size to keep [3]
mcode=T/F : Perform MCODE clustering [False]
xgmml=T/F : Output network in XGMML style [False]
xdir=PATH : Directory for XGMML output [./XGMML]

Layout Options

layout=X : Layout to be used for XGMML output [spring]
walltime=X : Walltime (hours) for layouts [0.02]
damping=X : Force Directed Layout, damping parameter [0.9]
colbydeg=T/F : Whether to colour PNG output by node degree [False]
nudgecyc=X : Number of cycles between node nudges (try to bump out of unstable equilibria) [1000]

MCODE Options

haircut=T/F : Whether to perform "haircut" on MCODE complexes [False]
multicut=T/F : Whether to perform "haircut" on MCODE complexes for the purposes of looking at nodes 2+ times [True]
fluff=X : MCODE "fluff" threshold. <0 = No Fluff [0.5]
vwp=X : MCODE vertex weighting percentage [0.2]
mink=X : MCODE min k-core values [2]
mindeg=X : MCODE min degree for node scoring [2]

See also rje.py generic commandline options.

History Module Version History

    # 2.0 - Initial Compilation from earlier version. Complete reworking, including generation of PPI Object.
    # 2.1 - Added method for generating subnetworks based on +/- scoring.
    # 2.2 - Minor misc modifications.
    # 2.3 - Added extra Complex options.
    # 2.4 - Added SVG output.
    # 2.5 - Minor tweaks to R output and walltime default.
    # 2.6 - Added addPPI(hub,spoke,evidence) method. Added nodelist option.
    # 2.7 - Added tabout=T/F Output PPI data as Node and Edge tables [False]
    # 2.8 - Tweaked Spring Layout. Stores original Hub and Spoke Field.
    # 2.8.1 - Fixed bug with Spring Layout interruption message.
    # 2.9.0 - Added ppiout=FILE : Save pairwise PPI file following processing (if rest=None) [None]

RJE_PPI REST Output formats

Run with &rest=docs for program documentation and options. A plain text version is accessed with &rest=help.
&rest=OUTFMT can be used to retrieve individual parts of the output, matching the tabs in the default
(&rest=format) output. Individual OUTFMT elements can also be parsed from the full (&rest=full) server output,
which is formatted as follows:

###~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~###
# OUTFMT:
... contents for OUTFMT section ...

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Available REST Outputs

There is currently no specific help available on REST output for this program.