[BioC] ggbio plot coverage adjusted for library size

Tengfei Yin tengfei.yin at sbgenomics.com
Tue Aug 26 21:58:01 CEST 2014

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.



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(<path to bamfiles>)
> 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
One Broadway FL 7
Cambridge, MA 02142
(617) 866-0446

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