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java.lang.Objectprocope.methods.interologs.InterologsCalculator
public class InterologsCalculator
Calculates interologs from a given set of binary interactions and a (homology) mapping between proteins. The basic assumption is that homologs of interacting proteins have a high probability of being interaction partners as well. These homology-derived potential interactors are then called interologs.
This class is not instantiatable.
Some ideas are adapted from
Yu, et. al
Annotation transfer between genomes: protein-protein interologs and protein-DNA regulogs.
Genome Res., 2004, 14, 1107-1118
Pubmed: 15173116
Method Summary | |
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static ProteinNetwork |
calculateInterologs(ProteinNetwork toTransfer,
ProteinNetwork mapping,
InterologScorer scorer)
Calculates interologs of an interaction network using a given protein mapping (which should contain homology information like bidirectional best hits). |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Method Detail |
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public static ProteinNetwork calculateInterologs(ProteinNetwork toTransfer, ProteinNetwork mapping, InterologScorer scorer)
The resulting network will have the directedness of the original interaction network.
The mapping network can be a directed network but will be used in an undirected manner.
toTransfer
- interaction network for which interologs will be calculatedmapping
- the protein mapping to be used, can be
BBHs
for instancescorer
- scorer for the interolog edges or null
to let all
transferred edges have a weight of 1.0
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