Question: 'downstream' disappeared from GenomicRanges package?
0
gravatar for Vang Le
8 months ago by
Vang Le70
Denmark
Vang Le70 wrote:

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?

 

genomicranges • 172 views
ADD COMMENTlink written 8 months ago by Vang Le70

There is a VariantAnnotation::downstream() function.

ADD REPLYlink written 8 months ago by Martin Morgan ♦♦ 23k

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 follow or precede do the job?

ADD REPLYlink modified 8 months ago • written 8 months ago by Vang Le70

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...

ADD REPLYlink written 8 months ago by Martin Morgan ♦♦ 23k
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