[BioC] In silico interactomes

maria at cbm.bio.uniroma2.it maria at cbm.bio.uniroma2.it
Thu Jun 22 20:15:40 CEST 2006

Dear Bioconductor mailing list,

I am explorying the two packages ScISI and y2hStat: the aim of these 
packages is to build an interactome starting from the available protein 
protein interaction datasets and combining them following a certain model. 
I would like to compare the interactome obtained with these packages with 
interactomes produced with other approaches and with a my own approach. 
These other putatives interactomes are generally in the format "proteinA proteinB";
now,my question is: 
how to go from the incidence matrix (the final output of the package 
ScISI) to this other kind of format without having the information about who was the 
bait and who was the prey?(I am interested in doing this with the merging 
result, the object ScISI.rda).

maybe a "solution" could be to transform the incidence matrix in a 
list of lists by doing....

for (i in 1:ncol(incidence.matrix)) {
   complexes.list$i <- list()
   comp <- rownames(exam[which(incidence.matrix[, i] == 1), i, drop =FALSE])

  and then apply the "matrix model" to every list 
component? but in this way the result is not comparable 
with the other interactomes generally based on the so called spoke 

thanks for your attention,



Maria Persico, PhD. student
MINT database group
Universita' di Tor Vergata, via della Ricerca scientifica 11
00133 Roma, Italy
Tel +39 0672594315 (Supervisor's room)
Fax +39 0672594766
Mobile phone: +393479715662
e-mail maria at cbm.bio.uniroma2.it

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