P. Terry,
When in doubt, first consult the manual pages. In particular
help("RleViewsList-class")
help(viewMaxs)
For example purposes, let's use the RleList object
> x <- RleList(a = c(0:10, 10L, 0:10), b = c(10:0, 10L, 10:0))
> islands <- slice(x, 1)
If you want the locations of the islands, use
> as(islands, "IRangesList")
CompressedIRangesList of length 2
$a
IRanges of length 2
start end width
[1] 2 12 11
[2] 14 23 10
$b
IRanges of length 2
start end width
[1] 1 10 10
[2] 12 22 11
If you want the locations of the maximums within each range, use
> viewRangeMaxs(islands)
SimpleIRangesList of length 2
$a
IRanges of length 2
start end width
[1] 11 12 2
[2] 23 23 1
$b
IRanges of length 2
start end width
[1] 1 1 1
[2] 12 13 2
Patrick
On 6/21/10 10:33 AM, [email protected] wrote:
Dear bioc-sig-sequencing,
Working through the workshop handout 'basicChipSeq.pdf' from URL:
http://www.bioconductor.org/workshops/2009/SeattleNov09/ChIP-seq/BasicChipSeq.pdf
page 3, I would like to access range information for a subset of the records in
an Rle object produced by for example,
cov.ctcf<- coverage(ctcf, width = mouse.chromlens, extend = 126L)
cov.ctcf$chr10
Then if run
islands<- slice(cov.ctcf$chr10, lower = 1)
islands
viewMaxs(head(islands))
would like to access subset of ranges associated with particular values in the
ViewMaxs(islands) output, for example,>= to a specified depth of reads.
Idea: if islands in 'islands' object are in same order as their associated
depth values in viewMaxs(islands) output vector, perhaps could loop through
viewMaxs(islands) vector of values, access/extract associated range from the
'islands' (Rle) object?
However, how to 'access' the range values from the 'islands' Rle object?
Perhaps there is a recomended way to achieve this goal?
Thanks,
P. Terry
[email protected]
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