Entering edit mode
Denise Scholtens
▴
70
@denisescholtens852
Last seen 9.8 years ago
Hi Maria,
I think your questions actually pertain more to the 'graph' package
rather
than GraphAT. A few quick fixes using some functions in the graph
package
should get you ready to use GraphAT. My answers to your questions
follow.
At 08:29 AM 9/6/2005, you wrote:
>Hello,
>
>I'm using GraphAT package to "measure" the congruency between an
>experimental dataset and the metadata GO biological process.
>
>my experimental dataset is small if compared with GO meta data.
>The specie on which I'm working is Yeast(cerevisiae).
>
>The important absumption with the method "getpvalue" of GraphAT
package is
>that the graphs that you want "compare" must have the same
nodes(obviously
>the number of edges should be different). If the 2 adj matrices you
want
>compare are different in size you get an error.
>
>In my specific case, I created a subset of the big GO meta data
file(in
>this subset I had only the nodes that were present in the
experimental
>dataset) and I tried to remove from this subset only the edges that
gave
>as similarity measures, values of Dij<3.I had 109 edges of this kind.
>
>So I did :
>
>for(i in 1:109){
>GgoPredYBPnew<removeEdge(as.character(edges.to.delete$V1[i]),
>as.character(edges.to.delete$V2[i]), GgoPredYBP)
> }
>
>but the graph that I obtained was only of one edge smaller!!!
>
>May somebody help me?
Note that GgoPredYBP is called in each iteration of the for loop as
the
graph from which to remove the edge. GgoPredYBPNew is not updated
with
each iteration. Your graph is only one edge smaller because at the
end of
the for loop, really only the 109th edge is removed. If you do update
your
new graph, then you will be able to remove all 109 edges.
>I would have also some other questions regarding this package:
>
>how to use the information about the edge weights? for
>example I want to consider as "common edges" between two graph only
>the ones that have a certain values in their edge weights....
I am not aware of a way to create a subgraph according to edge weights

although one may certainly exist! I think what I would do is get the
list
of edge weights using edgeWeights() in the graph package and then set
up a
similar loop to what you have above, making sure to update the graph
each
time.
>If the graphs that I want to compare have a different set of nodes
(some
>in common ), does some method could be developed to work directly
only
>with nodes in common?
The GraphAT package is not currently set up only to work on the common
nodes. I think the easiest thing to do for now would be to use the
subGraph function in the graph package. If you identify the common
set of
nodes, then create a subgraph for each of the two graphs using that
set of
nodes. You should be all set.
I hope that helps.
Denise
>thanks for your attention.
>
>
>maria
>
>
>
>Maria Persico
>MINT database, Cesareni Group
>Universita' di Tor Vergata, via della Ricerca Scientifica
>00133 Roma, Italy
>Tel: +39 0672594315
>FAX: +39 0672594766
>email: maria at cbm.bio.uniroma2.it
>
>_______________________________________________
>Bioconductor mailing list
>Bioconductor at stat.math.ethz.ch
>https://stat.ethz.ch/mailman/listinfo/bioconductor
**********************************************************************
Denise Scholtens, Ph.D.
Northwestern University Medical School
Department of Preventive Medicine
680 N. Lake Shore Drive Suite 1102
Chicago, IL 60611
312.503.7261
312.908.9588 (fax)
dscholtens at northwestern.edu