Martin, thanks for the input and suggestion about views, that's very helpful
to know.

Andrew

On Wed, Jun 23, 2010 at 6:55 PM, Martin Morgan <mtmorgan@fhcrc.org> wrote:

> Hi Andrew --
>
> On 06/23/2010 02:02 PM, Andrew Yee wrote:
> > Hi, I'm trying to figure out the coverage for a specific range.
> >
> > Take for example,
> >
> > r <- IRanges(start = c(30, 60, 70, 100), width = c(20, 18, 20, 18))
> >
> > I'm interested in the coverage from positions 60 to 65, which in this
> case
> > is 1.  I'm also interested in the coverage say from positions 68 to 73,
> > which goes from 1 to 2.
> >
> > While I can use coverage(r) and then use runLength() and runValue() to
> > ultimately extract this information, is there a way to use coverage so
> that
> > you can directly specify the positions of interest?
>
> One possibility is to create views onto your coverage vector
>
>   r <- IRanges(start = c(30, 60, 70, 100), width = c(20, 18, 20, 18))
>   roi = IRanges(c(60, 68), width=5)  ## 'regions of interest'
>  v = Views(coverage(r), roi)
>
> and then do all sorts of fun things, like home movies
>
>  for (i in seq_len(length(v))) plot(as.integer(v[[i]]), type="l")
>
> Martin
>
> >
> > Thanks,
> > Andrew
> >
> >> sessionInfo()
> > R version 2.11.0 (2010-04-22)
> > x86_64-unknown-linux-gnu
> >
> > locale:
> >  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
> >  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
> >  [5] LC_MONETARY=C              LC_MESSAGES=en_US.UTF-8
> >  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
> >  [9] LC_ADDRESS=C               LC_TELEPHONE=C
> > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
> >
> > attached base packages:
> > [1] stats     graphics  grDevices utils     datasets  methods   base
> >
> > other attached packages:
> > [1] IRanges_1.6.0
> >
> > loaded via a namespace (and not attached):
> > [1] tools_2.11.0
> >
> >       [[alternative HTML version deleted]]
> >
> > _______________________________________________
> > Bioc-sig-sequencing mailing list
> > Bioc-sig-sequencing@r-project.org
> > https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
>
>
> --
> Martin Morgan
> Computational Biology / Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N.
> PO Box 19024 Seattle, WA 98109
>
> Location: Arnold Building M1 B861
> Phone: (206) 667-2793
>

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