[BioC] Creating a custom chromLocation object for cPlot

[Michael Muratet]

Greetings

I am trying to create a custom chromLocation object from RNA-seq data  
aligned against the UCSC knownGene table for plotting with cPlot.  The  
quickest way I see to do that is to assemble it from the expression  
results. If I look at chromLocs(buildChromLocation("org.Mm.eg")) I see  
(for example)

$`9`
  100009600  100036537  100039707  100040259  100041096  100041605   
100041618  100042265  100042314
  -20866836   49326392  -88583442  -14649687  106528912  -35656129   
-35941871 -121758657   78137734
  100042464  100042485  100216535  100217453  100312948  100312949   
100312956  100312986  100312987

from which I deduce that the first 8 values could be four pairs. But  
that leaves 100042314 -20866836. What is the format for this list?

Also, is there an easier way to go about this?

Thanks

Mike

Michael Muratet, Ph.D.
Senior Scientist
HudsonAlpha Institute for Biotechnology
mmuratet at hudsonalpha.org
(256) 327-0473 (p)
(256) 327-0966 (f)

Room 4005
601 Genome Way
Huntsville, Alabama 35806