Hi! I'm trying to debug the cosmo R package because I'm trying to find out
where all the motifs are.
I display some of them printing the "motif" variable but I don't know how
to show all of the found motifs in one run.

http://www.bioconductor.org/packages/2.10/bioc/html/cosmo.html

I think that they must be in line 366 in "sites" variable in cosmo.R:

 Code:

for (i in 1:com$selNumSites){
      site <- seqMat[com$alignStarts[i]:(com$alignStarts[i]+com$selWidth-1),
                     com$alignSeqs[i]]
      sites <- c(sites, toString(site))

But when I try to debug it I need first to load the cosmo library, then
read the data and then run cosmo:

 Code:

library(cosmo)
seqal <- system.file("Exfiles/short702k.FASTA", package="cosmo")
res <- cosmo(seqs=seqal, constraints="None", minW=10, maxW=10, models="TCM" )



For debugging line 366 I think I should:
 Code:

library(cosmo)
seqal <- system.file("Exfiles/short702k.FASTA", package="cosmo")
setBreakpoint("cosmo.R",366)
res <- cosmo(seqs=seqal, constraints="None", minW=10, maxW=10, models="TCM" )

But I don't get any value of any variable..

And it doesn't seem to be the easiest way to get the sites variable values..

Ana

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