Entering edit mode
I have a legacy script using `downstream` function which I believe it is from GenomicRanges package. I may be wrong, then I would like to know the correct package to use. I found out about this after updating to bioconductor version 3.6 (see full sessioninfo below).
> sessionInfo() R version 3.4.4 (2018-03-15) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 16.04.4 LTS Matrix products: default BLAS: /usr/lib/openblas-base/libblas.so.3 LAPACK: /usr/lib/libopenblasp-r0.2.18.so locale: [1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8 [5] LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=en_GB.UTF-8 [7] LC_PAPER=en_GB.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] parallel stats4 stats graphics grDevices utils datasets [8] methods base other attached packages: [1] GenomicRanges_1.30.3 GenomeInfoDb_1.14.0 IRanges_2.12.0 [4] S4Vectors_0.16.0 BiocGenerics_0.24.0 loaded via a namespace (and not attached): [1] zlibbioc_1.24.0 compiler_3.4.4 XVector_0.18.0 [4] tools_3.4.4 GenomeInfoDbData_1.0.0 RCurl_1.95-4.10 [7] bitops_1.0-6
after the update, `downstream` is not found. If the function is removed, shouldn't be a deprecation warning?
There is a VariantAnnotation::downstream() function.
Thank you Martin. I will look into that function but I am hesitated to use it before finding some better solution. This is because I don't work anything with variants for this data. Can
followorprecededo the job?Have you told us what version you think there was a GenomicRanges::downstream() function? Not much point saying that precede / follow are comparable without knowing what to compare with...