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 <[email protected] <mailto:[email protected]>>
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
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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: [email protected]
Phone: (206) 667-5791
Fax: (206) 667-1319
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