I have some code using snpsById from SNPlocs which worked under R 3.4.4/Bioconductor 3.6 which has now broken since upgrading to R-3.5.0/Bioconductor 3.7. I've not been able to find any documented change which may be responsible for this. The following snippet illustrates the problem:
library("SNPlocs.Hsapiens.dbSNP144.GRCh37") snps<-c("rs429358"); snplocs<-SNPlocs.Hsapiens.dbSNP144.GRCh37 locs<-snpsById(snplocs, snps) positions<-lapply(locs,pos)
This used to return a list of SNP positions, but now reports:
Error in (function (classes, fdef, mtable) : unable to find an inherited method for function ‘getListElement’ for signature ‘"GPos"’
I've searched http://bioconductor.org/news/bioc_3_7_release/ for changes to GPos but can't see anything. I know I can use as.data.frame which is probably the simplest fix, but I'm interested to know why this no longer works.
SessionInfo() output pasted below...
Many thanks James
R version 3.5.0 (2018-04-23) Platform: x86_64-apple-darwin15.6.0 (64-bit) Running under: macOS High Sierra 10.13.4 Matrix products: default BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib LAPACK: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib locale:  en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8 attached base packages:  stats4 parallel stats graphics grDevices utils datasets methods base other attached packages:  SNPlocs.Hsapiens.dbSNP144.GRCh37_0.99.20 BSgenome_1.48.0 rtracklayer_1.40.2  Biostrings_2.48.0 XVector_0.20.0 GenomicRanges_1.32.2  GenomeInfoDb_1.16.0 IRanges_2.14.8 S4Vectors_0.18.1  BiocGenerics_0.26.0 loaded via a namespace (and not attached):  zlibbioc_1.26.0 GenomicAlignments_1.16.0 BiocParallel_1.14.1 lattice_0.20-35  tools_3.5.0 SummarizedExperiment_1.10.1 grid_3.5.0 Biobase_2.40.0  matrixStats_0.53.1 yaml_2.1.19 Matrix_1.2-14 GenomeInfoDbData_1.1.0  bitops_1.0-6 RCurl_1.95-4.10 DelayedArray_0.6.0 compiler_3.5.0  Rsamtools_1.32.0 XML_3.98-1.11