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 [[alternative HTML version deleted]] ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
