Entering edit mode
Tengfei Yin
▴
490
@tengfei-yin-6162
Last seen 10.3 years ago
Hey James,
So sorry for the late reply, in case I forget, you can also leave your
question/feedback ingithub issues page backlog
<https: github.com="" tengfei="" ggbio="" issues="">. I will work on those
backlogs
when I got time.
Are you looking for a normalization cross samples for
coverage? Unfortunately, it's not built-in yet.
But I am re-work on autoplot() for bamfile list for particular regions
now,
I will think about give options on normalization considering the
library
size. Or more flexible, you could use your own method to do
normalization
on the raw RleList, then autoplot will provide better/faster graphics
for
RleList after the improvements. This new features will be implemented
in
devel branch.
Let's keep in touch.
cheers
Tengfei
On Wed, Jul 9, 2014 at 5:26 PM, James W. MacDonald <jmacdon at="" uw.edu="">
wrote:
> Hi,
>
> Is there an easy way to adjust the coverage plots for library size?
As an
> example, if I do
>
> library(ggbio)
> library(Rsamtools)
> which <- GRanges("chr12", IRanges(29358072, 29367039))
> bfl <- BamFileList()
> p1 <- autoplot(TxDb.Mmusculus.UCSC.mm9.knownGene, which=which)
> p2 <- autoplot(bfl, which=which)
> c(tracks(p1), p2)
>
> I get almost what I want, but the plot is misleading because the
coverage
> is dependent on the library size, and I would like to account for
that
> fact. Is there some way to incorporate the library size in the
computation
> of the coverage? In other words, I would rather plot
coverage/million reads
> or similar.
>
> Thanks,
>
> Jim
>
>
> --
> James W. MacDonald, M.S.
> Biostatistician
> University of Washington
> Environmental and Occupational Health Sciences
> 4225 Roosevelt Way NE, # 100
> Seattle WA 98105-6099
>
> _______________________________________________
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>
--
Tengfei Yin, PhD
Product Manager
Seven Bridges Genomics
sbgenomics.com
One Broadway FL 7
Cambridge, MA 02142
(617) 866-0446
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