[BioC] Problems with k-cliq definition and calculations using RBGL package

[Chanchal Kumar]

Dear All,

    I am using RBGL package to find k-cliq in a graph as per the
definition given by the recent review by Huber et al. 

http://www.biomedcentral.com/1471-2105/8/S6/S8

As per the paper "A k-clique is a subgraph with nodes Vs such that the
distance d(v, u) between nodes v and u is less than or equal to k for
all nodes v, u belonging to Vs."

I find all the k-cliques in the graph using the code below:

>library("RBGL")
>library("yeastExpData")
>data("litG")

>litG

# the return value of kCliques is a list whose k-th entry is a list of
all the k-cliques in the graph.
>kcliq = kCliques(litG)

But then I see that the set of 9-cliques have sub graphs which have only
4 nodes. I am now confused how this can be possible? For example see
this third 9-clique and it has only 4 nodes(code below). Then how can
such a sub graph be 9-clique. I will appreciate any insights on this
issue.

# Now extracting the 3rd 9-clique...
>kcliq[[9]][3]
[[1]]
[1] "YDL140C" "YNL251C" "YPL228W" "YGL130W"


Best Regards,
Chanchal 
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Chanchal Kumar, Ph.D. Candidate
Dept. of Proteomics and Signal Transduction
Max Planck Institute of Biochemistry
Am Klopferspitz 18
82152 D-Martinsried (near Munich)
Germany
e-mail: chanchal at biochem.mpg.de
Phone: (Office) +49 (0) 89 8578 2296
Fax:(Office) +49 (0) 89 8578 2219
http://www.biochem.mpg.de/mann/
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