Thanks Herve, that's very helpful, and that does answer my question.
 Thanks.

Andrew

2010/6/28 Hervé Pagès <hpages@fhcrc.org>

> 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@fhcrc.org <mailto:hpages@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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>>        <mailto:Bioc-sig-sequencing@r-project.org>
>>
>>        https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
>>
>>
>>
>>
>
> --
> 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@fhcrc.org
> Phone:  (206) 667-5791
> Fax:    (206) 667-1319
>

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