[BioC] Creating a custom chromLocation object for cPlot
Michael Muratet
mmuratet at hudsonalpha.org
Thu Aug 19 16:59:02 CEST 2010
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
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