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

[Hervé Pagès]

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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