[Bioc-sig-seq] coverage() in IRanges

[Martin Morgan]

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]]
> 
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-- 
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