On Wed, Feb 19, 2014 at 8:39 AM, Jesper Gådin <jesper.ga...@gmail.com>wrote:
> Hi Michael,
>
> Herves suggestion will probably work for my use case, but if there are any
> smoother ways it would be preferable.
>
> The use case is as follows:
>
> 1) calculate strand specific coverage over a region from
> GAlignments object (or file)
>
> At the moment I read a file using readGAlignmentsFromBam() with tag="XS",
> then filter it on "flag" and "mapq". Then I subset the
> resulting GAlignments in a minus and a plus -strand object.
> Then I calculate coverage by my own coverage function which uses the cigar
> information in the GAlignments object. This function is the one using
> cigarToRleList() at the moment. As I understand the coverage() function
> from the GenomicAlignments/IRanges package does not take into account
> cigars, or does it?
>
>
It does take the coverage into account; specifically to exclude the introns
from coverage. I think there's also an option to exclude deletions.
> I started to look at the applyPileups() in Rsamtools which I can get to
> calculate coverage using cigars, but not using the strand or flag
> information for filtering. That solution would start from a bam-file
> instead of a GAlignments object, and sure I can do the filtering outside R.
> But it would be very convenient to do it all from within R.
>
> If there are nice solutions starting from both a GAlignments and a
> bam-file it would be great! =)
>
> /Jesper
>
>
>
> On Tue, Feb 18, 2014 at 10:52 PM, Michael Lawrence <
> lawrence.mich...@gene.com> wrote:
>
>> Hi Jesper,
>>
>> Would you be willing to volunteer your use case? As Herve hinted,
>> cigarToRleList and friends are low-level helpers. There may be an easier
>> way to achieve what you want, or an opportunity to improve things.
>>
>> Michael
>>
>>
>> On Mon, Feb 17, 2014 at 1:10 AM, Jesper Gådin <jesper.ga...@gmail.com>wrote:
>>
>>> Hi,
>>>
>>> Have come across a cigar-vector that is problematic to process.
>>>
>>> #load package
>>> > library(GenomicAlignments)
>>>
>>> #load data (see attached file)
>>> > load("2014-02-17-cigarExample.rdata")
>>>
>>> #run function cigarToRleList
>>> > cigarRle <- cigarToRleList(cigarExample)
>>> Error in .Call2("Rle_constructor", values, lengths, check, 0L, PACKAGE =
>>> "IRanges") :
>>> integer overflow while summing elements in 'lengths'
>>>
>>> > sessionInfo()
>>> R Under development (unstable) (2013-11-13 r64209)
>>> Platform: x86_64-unknown-linux-gnu (64-bit)
>>>
>>> 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=en_US.UTF-8 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] parallel stats graphics grDevices utils datasets methods
>>> [8] base
>>>
>>> other attached packages:
>>> [1] GenomicAlignments_0.99.18 Rsamtools_1.15.26
>>> [3] Biostrings_2.31.12 XVector_0.3.6
>>> [5] GenomicRanges_1.15.26 IRanges_1.21.23
>>> [7] BiocGenerics_0.9.3
>>>
>>> loaded via a namespace (and not attached):
>>> [1] BatchJobs_1.1-1135 BBmisc_1.5 BiocParallel_0.5.8
>>> bitops_1.0-6
>>>
>>> [5] brew_1.0-6 codetools_0.2-8 DBI_0.2-7
>>> digest_0.6.4
>>>
>>> [9] fail_1.2 foreach_1.4.1 iterators_1.0.6 plyr_1.8
>>>
>>> [13] RSQLite_0.11.4 sendmailR_1.1-2 stats4_3.1.0 tools_3.1.0
>>>
>>> [17] zlibbioc_1.9.0
>>>
>>> _______________________________________________
>>> Bioc-devel@r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>
>>>
>>
>
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