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

[Hervé Pagès]

Hi Andrew,

On 06/27/2010 08:30 PM, Andrew Yee wrote:
> Herve, thanks for your help.  To follow up some more, is there a way to
> directly specify the start and end in coverage(), without using shift
> and width?

No, you need to use shift and width. However, translating your
start/end into shift/width is straightforward. If you have the
start and end, do:

   coverage(r, shift=1-start, width=end-start+1)

>
> Or alternatively, as Martin suggests,
>
> 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)
>
> but in this case, extract the coverage information from v in the above
> example?

'v' is a set of views defined on the full coverage vector for 'r':

   > v
   Views on a 117-length Rle subject

   views:
       start end width
   [1]    60  64     5 [1 1 1 1 1]
   [2]    68  72     5 [1 1 2 2 2]

To extract the coverage spanning the i-th view, use v[[i]]:

   > v[[1]]
   'integer' Rle of length 5 with 1 run
     Lengths: 5
     Values : 1
   > v[[2]]
   'integer' Rle of length 5 with 2 runs
     Lengths: 2 3
     Values : 1 2

Does this answer your question?

H.

>
> Thanks,
> Andrew
>
>
> 2010/6/25 Hervé Pagès <hpages at fhcrc.org <mailto:hpages at fhcrc.org>>
>
>     Hi Andrew,
>
>     One way to specify directly the window of interest when calling
>     coverage() is to use the 'shift' and 'width' arguments.
>     'shift' allows you to shift the ranges contained in the first
>     argument to the left (negative shift) or to the right (positive
>     shift) before extracting the coverage:
>
>     ## Coverage from positions 60 to 65:
>      > as.integer(coverage(r, shift=-59, width=6))
>     [1] 1 1 1 1 1 1
>
>     ## Coverage from positions 68 to 73:
>      > as.integer(coverage(r, shift=-67, width=6))
>     [1] 1 1 2 2 2 2
>
>     Note that coverage(r, shift=-59, width=6) is equivalent to
>     coverage(shift(r, -59), width=6).
>
>     Cheers,
>     H.
>
>
>
>     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?
>
>         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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>
>
>


-- 
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M2-B876
P.O. Box 19024
Seattle, WA 98109-1024

E-mail: hpages at fhcrc.org
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