findOverlaps
in the GenomicRanges
package has a flag, ignore.strand=TRUE
, which allows the overlap computation to use only the duple (seqnames,ranges)
, essentially ignoring the strand. Is there a way to use findOverlaps
to ignore seqnames
so that only the duple (ranges,strand)
is used to compute an overlap? If not, is there another way to compute overlaps using only (ranges,strand)
?
Any pointers will be gratefully received.
> sessionInfo()
R version 3.6.1 (2019-07-05)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.3 LTS
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.7.1
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.7.1
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 stats4 stats graphics grDevices utils datasets
[8] methods base
other attached packages:
[1] GenomicRanges_1.36.1 GenomeInfoDb_1.20.0 IRanges_2.18.2
[4] S4Vectors_0.22.1 BiocGenerics_0.30.0
loaded via a namespace (and not attached):
[1] zlibbioc_1.30.0 compiler_3.6.1 XVector_0.24.0
[4] GenomeInfoDbData_1.2.1 RCurl_1.95-4.12 bitops_1.0-6
Would you please provide more details on the use case?