 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
pterry@huskers.unl.edu

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