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?
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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