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Last seen 10.2 years ago
Hi,
I was wondering whether it is possible in anyway to obtain the overlap
coordinates when intersecting GAlignments objects as query with a
GRangesList object, using the findSpliceOverlaps function?
Specifically, I would like to obtain the transcriptomic coordinates of
the GAlignments in the transcripts that they compatibly intersect
with.
Right now I'm obtaining this information in a 2 step approach:
1. findSpliceOverlaps(GAlignments, GRangesList, ignore.strand=FALSE)
2. Keeping only the hits that are compatible, I then intersect again
each GAlignment and the ranges of the compatible GRange transcript and
sum the widths of the exons up to the intersection coordinate.
My problem is that the second step is extremely slow.
I'd be grateful for some discussion
-- output of sessionInfo():
R version 3.0.2 (2013-09-25)
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] hash_2.2.6 data.table_1.8.10 Rsamtools_1.14.3
[4] Biostrings_2.30.1 GenomicRanges_1.14.4 XVector_0.2.0
[7] IRanges_1.20.6 BiocGenerics_0.8.0
loaded via a namespace (and not attached):
[1] bitops_1.0-6 stats4_3.0.2 tools_3.0.2 zlibbioc_1.8.0
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