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
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