bg.order =  num 3
big.memory =  logi FALSE
big.memory.verbose =  logi FALSE
cluster.rows.allowed =  num [1:2] 3 70
cmonkey.filename =  chr "cmonkey_4.8.8_mmp_1661x58_11_Oct_11_16:14:07"
cmonkey.version =  chr "4.8.8"
cm.script.each.iter =  chr "cm.script.each.iter.R"
cog.org =  chr "Mmp"
col.iters =  num [1:400] 1 6 11 16 21 26 31 36 41 46 ...
date.run =  chr "11 Oct 11 16:14:07"
dust.cmd =  chr "./progs//dust $fname"
fuzzy.index =  num [1:2000] 0.749 0.748 0.747 0.746 0.745 ...
grouping.weights =  num(0) 
k.clust =  num 166
maintain.seed =  NULL
mast.cmd =  chr "./progs//mast $memeOutFname -d $fname -bfile $bgFname -nostatus -stdout -text -brief -ev 99999 -mev 99999 -mt 0.99 -seqp -remco"| __truncated__
max.changes =  Named num [1:2] 0.5 5
 - attr(*, "names")= chr [1:2] "rows" "cols"
meme.cmd =  chr "./progs//meme $fname -bfile $bgFname -psp $pspFname -time 600 -dna -revcomp -maxsize 9999999 -nmotifs %1$d -evt 1e9 -minw 6 -ma"| __truncated__
meme.iters =  num [1:45] 600 700 800 900 1000 1100 1200 1250 1300 1350 ...
merge.cutoffs =  Named num [1:2] 0.3 0.975
 - attr(*, "names")= chr [1:2] "n" "cor"
motif.upstream.scan =  num [1:2] -30 250
motif.upstream.search =  num [1:2] -20 150
mot.iters =  num [1:467] 601 604 607 610 613 616 619 622 625 628 ...
mot.scaling =  num [1:1500] 0 0.000667 0.001334 0.002001 0.002668 ...
mot.weights =  Named num 1
 - attr(*, "names")= chr "upstream meme"
n.clust.per.col =  num 111
n.clust.per.row =  num 2
net.iters =  num [1:286] 1 8 15 22 29 36 43 50 57 64 ...
net.scaling =  num [1:1500] 0 0.000334 0.000667 0.001001 0.001334 ...
net.weights =  Named num [1:2] 0.5 0.5
 - attr(*, "names")= chr [1:2] "string" "operons"
n.iter =  num 2000
n.motifs =  num [1:1334] 1 1 1 1 1 1 1 1 1 1 ...
no.genome.info =  logi FALSE
operon.shift =  logi TRUE
organism =  chr "mmp"
parallel.cores =  num 1
parallel.cores.motif =  num 1
plot.iters =  num [1:80] 2 27 52 77 102 127 152 177 202 227 ...
post.adjust =  logi TRUE
progs.dir =  chr "./progs/"
recalc.bg =  logi TRUE
rnd.seed =  int 407213692
row.iters =  num [1:1000] 1 3 5 7 9 11 13 15 17 19 ...
row.scaling =  num 6
row.weights =  Named num 1
 - attr(*, "names")= chr "ratios"
rsat.species =  chr "Methanococcus_maripaludis_S2"
rsat.urls =  chr [1:3] "http://rsat.ccb.sickkids.ca/" "http://rsat.ulb.ac.be/rsat/" ...
save.logfile =  logi FALSE
seed.method =  Named chr [1:2] "kmeans" "best"
 - attr(*, "names")= chr [1:2] "rows" "cols"
session.info =  Named chr [1:111] "x86_64-unknown-linux-gnu" "x86_64" "linux-gnu" ...
 - attr(*, "names")= chr [1:111] "platform" "arch" "os" "system" ...
stats.iters =  num [1:401] 1 5 10 15 20 25 30 35 40 45 ...
taxon.id =  int 39152
time.ended =  chr "Wed Oct 12 05:41:02 2011"
time.started =  chr "Tue Oct 11 16:14:07 2011"
translation.tab =  NULL