R help - Nov 2012 - GraphNEL object retrieve edgenumber from acc() or is it list of lists?

Hello everyone,

Im working with graphNEL object and want to extract all the nodes which 
have adjacent nodes with at least 20 nodes in between them.

acc(graph, graphnodes) obviously provides a list for the accessable
nodes of every node from a node and a number of the edges between them. 
Like this:

$`hsa:8379`
hsa:100131844     hsa:10393    hsa:246184     hsa:29882     hsa:29945 
            1             1             1             1             1 
    hsa:51433     hsa:51434     hsa:51529     hsa:64682      hsa:8697 
            1             1             1             1             1 

$`hsa:51343`
hsa:23594 hsa:23595  hsa:5001  hsa:5000  hsa:4999  hsa:4998  
        8         8         8         8         8         8 

and so on. However I want know access the numbers so that I can compare
these
edgenumbers and only retrieve the nodes with an accessable node with at
least
20 edges as mentioned above. How can I achieve this? In addtion whats the
data
type of the result of acc(). Is it a list in a list? 

Thank you




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On 11/01/2012 01:23 PM, risclab wrote:
> Hello everyone,
>
> Im working with graphNEL object and want to extract all the nodes which
> have adjacent nodes with at least 20 nodes in between them.
>
> acc(graph, graphnodes) obviously provides a list for the accessable
> nodes of every node from a node and a number of the edges between them.
> Like this:
>
> $`hsa:8379`
> hsa:100131844     hsa:10393    hsa:246184     hsa:29882     hsa:29945
>              1             1             1             1             1
>      hsa:51433     hsa:51434     hsa:51529     hsa:64682      hsa:8697
>              1             1             1             1             1
>
> $`hsa:51343`
> hsa:23594 hsa:23595  hsa:5001  hsa:5000  hsa:4999  hsa:4998
>          8         8         8         8         8         8
>
> and so on. However I want know access the numbers so that I can compare
> these
> edgenumbers and only retrieve the nodes with an accessable node with at
> least
> 20 edges as mentioned above. How can I achieve this? In addtion whats the
> data
> type of the result of acc(). Is it a list in a list?
Hi -- best to ask questions about Bioconductor packages on the Bioconductor 
mailing list.

http://bioconductor.org/help/mailing-list/

The help page ?acc says

Value:

      The methods should return a named list of integer vectors. The
      'names' of the list correspond to the names of the supplied nodes.

and for a reproducible example after

 > example(acc)

we have

 > class(acc(gR3, "A"))
[1] "list"
 > class(acc(gR3, "A")[[1]])
[1] "numeric"

so the return type is a named list of named numeric vectors. as(gR3,
"matrix")
might also provide an easily computable structure.

Martin
>
> Thank you
>
>
>
>
> --
> View this message in context:
http://r.789695.n4.nabble.com/GraphNEL-object-retrieve-edgenumber-from-acc-or-is-it-list-of-lists-tp4648174.html
> Sent from the R help mailing list archive at Nabble.com.
>
> ______________________________________________
> R-help at r-project.org mailing list
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> PLEASE do read the posting guide
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> and provide commented, minimal, self-contained, reproducible code.
>

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