[BioC] finding cliques with packages Graph and RBGL

[lilong at isb-sib.ch]

Hi,

Could you provide the dataset?  Without any further info, it's hard to
judge the results, especially the graph changes dynamically.  For instance
it's possible that at SOME stage, there is no bigger clicks.

If you provide a graph that shows the behaviour (that particular graph),
we could help further.

Thanks

Li

> Hello everyone,
>
> I am using packages Graph and RBGL 1.8 with R 2.3.1 for finding cliques in
> a
> undirected dynamical graph (it changes over time).
> What I do: I load data (adjacency matrix for Graph) from database in a
> temporal step.
> I transform the matrix in a direct graph using ftM2graphNEL, I make some
> analysis (like "degree"), then I transform the
> direct graph in a undirect graph using "ugraph" to use maxClique to find
> all
> the cliques in this graph (which now is undirect).
> But I found a problem: in some steps the output of maxClique give me only
> clique of length one...but it is a graph with density
> near at 1! In the step before it gives me one or two cliques of lenght 27
> or
> 28 (the node in the graph are 29).
> I give you some outputs:
>
> step "Before":
>
> $maxCliques
> $maxCliques[[1]]
>  [1] "1"  "3"  "6"  "7"  "8"  "9"  "11" "12" "14" "16" "17" "18" "19" "20"
> "21"
> [16] "24" "25" "27" "30" "31" "32" "35" "36" "37" "39" "40" "33" "26"
>
> $maxCliques[[2]]
>  [1] "1"  "3"  "6"  "7"  "8"  "9"  "11" "12" "14" "16" "17" "18" "19" "20"
> "21"
> [16] "24" "25" "27" "30" "31" "32" "35" "36" "37" "39" "40" "22"
>
> the degree (in the undirected graph) of each node is (node are number from
> 1
> to 40, but in time some node (e.g.  node 2) "dies"):
>
>  1  3  6  7  8  9 11 12 14 16 17 18 19 20 21 22 24 25 26 27 30 31 32 33 35
> 36
> 28 28 28 28 28 28 28 28 28 28 28 28 28 28 28 26 28 28 27 28 28 28 28 27 28
> 28
> 37 39 40
> 28 28 28
>
> and in the "next" step the output is the following:
>
> $maxCliques
>       [,1] [,2]
>  [1,] "1"  "1"
>  [2,] "3"  "3"
>  [3,] "6"  "6"
>  [4,] "7"  "7"
>  [5,] "8"  "8"
>  [6,] "9"  "9"
>  [7,] "11" "11"
>  [8,] "12" "12"
>  [9,] "14" "14"
> [10,] "16" "16"
> [11,] "17" "17"
> [12,] "18" "18"
> [13,] "19" "19"
> [14,] "20" "20"
> [15,] "21" "21"
> [16,] "24" "24"
> [17,] "25" "25"
> [18,] "26" "26"
> [19,] "27" "27"
> [20,] "30" "30"
> [21,] "31" "31"
> [22,] "32" "32"
> [23,] "35" "35"
> [24,] "36" "36"
> [25,] "37" "37"
> [26,] "39" "39"
> [27,] "40" "40"
> [28,] "33" "22"
>
> The number of node in each cliques in always 1.
>
> degree:
>  1  3  6  7  8  9 11 12 14 16 17 18 19 20 21 22 24 25 26 27 30 31 32 33 35
> 36
> 28 28 28 28 28 28 28 28 28 28 28 28 28 28 28 27 28 28 28 28 28 28 28 27 28
> 28
> 37 39 40
> 28 28 28
>
> Some ideas?
> Thank-you very much.
>
> Sorry for my english.
>
> Davide
>
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