bg.order = [1] 3
cluster.rows.allowed = [1]  3 70
cmonkey.filename = [1] "cmonkey_4.1.5_sce_4478x667_09_Oct_09_04:03:18"
cmonkey.session.info =                                                         platform 
                                        x86_64-unknown-linux-gnu 
                                                            arch 
                                                          x86_64 
                                                              os 
                                                       linux-gnu 
                                                          system 
                                               x86_64, linux-gnu 
                                                          status 
                                                                 
                                                           major 
                                                               2 
                                                                 
                                                             ... 
                                          loadedOnly.tools.Title 
                                   Tools for Package Development 
                                         loadedOnly.tools.Author 
                                Kurt Hornik and Friedrich Leisch 
                                     loadedOnly.tools.Maintainer 
                              R Core Team <R-core@r-project.org> 
                                    loadedOnly.tools.Description 
Tools for package development, administration and\ndocumentation 
                                        loadedOnly.tools.License 
                                                 Part of R 2.9.0 
                                          loadedOnly.tools.Built 
R 2.9.0; x86_64-unknown-linux-gnu; 2009-06-04 16:43:12 UTC; unix 
cmonkey.time.ended = [1] "Sat Oct 10 12:49:49 2009"
cmonkey.time.started = [1] "Fri Oct  9 04:03:18 2009"
cmonkey.version = [1] "4.1.5"
cog.org = [1] "Sce"
date.run = [1] "09 Oct 09 04:03:18"
fuzzy.index =  [1] 0.7485014990005     0.747005992007994   0.745513473040451  
 [4] 0.744023936127795   0.742537375311876   0.741053784646448  
 [7] ...                 0.00187774803765157 0.00187399629456993
[10] 0.00187025204747597 0.00186651528139269 0.00186278598137302
[13] 0.00185906413249977
grouping.weights = chip.chip 
        1 
k.clust = [1] 300
mast.addl.args = [1] "-ev 99999 -mev 99999 -mt 0.99 -seqp -remcorr"
mast.cmd = [1] "progs/mast"
max.changes = rows cols 
 0.2  5.0 
meme.addl.args = [1] "-time 600 -maxsize 9999999 -nmotifs %1$d -evt 1e9 -minw %2$d -maxw %3$d -mod zoops"
meme.cmd = [1] "progs/meme"
meme.consensus = [1] "compute"
meme.consensus.e.val.limit = [1] 0.1
meme.seqs.allowed = [1]  3 70
merge.cutoffs =     n   cor 
0.300 0.975 
mot.iters =  [1] 100  200  300  400  500  600  ...  2500 2600 2700 2800 2900 3000
mot.scaling =  [1] 0                    0.000166777851901267 0.000333555703802535
 [4] 0.000500333555703802 0.00066711140760507  0.000833889259506338
 [7] ...                  0.249166110740494    0.249332888592395   
[10] 0.249499666444296    0.249666444296197    0.249833222148099   
[13] 0.25                
motif.palindrome.option = [1] "non"
motif.upstream.scan = [1] -30 250
motif.upstream.search = [1] -30 250
motif.width.range = [1]  6 24
n.clust.per.col = [1] 200
n.clust.per.row = [1] 2
n.iter = [1] 3000
n.motifs =  [1] 1   1   1   1   1   1   ... 2   2   2   2   2   2  
net.iters =  [1] 1    8    15   22   29   36   ...  2962 2969 2976 2983 2990 2997
net.scaling =  [1] 0                    6.6711140760507e-05  0.000133422281521014
 [4] 0.000200133422281521 0.000266844563042028 0.000333555703802535
 [7] ...                  0.0996664442961975   0.099733155436958   
[10] 0.0997998665777185   0.099866577718479    0.0999332888592395  
[13] 0.1                 
net.weights =    string   pp.ints bind.ints chip.chip 
     0.25      0.50      0.10      1.00 
no.genome.info = [1] FALSE
operon.shift = [1] FALSE
organism = [1] "sce"
parallel.cores = [1] 5
pareto.adjust.scalings = [1] TRUE
penalize.probes.without.seqs = [1] TRUE
plot.iters = [1] 0
post.adjust = [1] FALSE
remove.low.complexity.subseqs = [1] TRUE
resid.iters =  [1] 1    3    5    7    9    11   ...  2989 2991 2993 2995 2997 2999
resid.scaling =  [1] 1   1   1   1   1   1   ... 1   1   1   1   1   1  
rnd.seed = [1] 1255086198
rsat.species = [1] "Saccharomyces_cerevisiae"
rsat.urls = [1] "http://rsat.ulb.ac.be/rsat/"         "http://rsat.ccb.sickkids.ca/"       
[3] "http://embnet.ccg.unam.mx/rsa-tools"
save.logfile = [1] FALSE
seed.method =           rows           cols 
"net=string:5"         "best" 
stats.iters =  [1] 1    5    10   15   20   25   ...  2975 2980 2985 2990 2995 3000
taxon.id = [1] 4932
translation.tab = NULL
uniquify.seqs = [1] TRUE