Open hpages opened 5 years ago
Even though the BSgenomeViews() constructor accepts a GPos object:
BSgenomeViews()
library(BSgenome) v <- BSgenomeViews("hg38", GPos("chrY:11001-12000")) v # BSgenomeViews object with 1000 views and 0 metadata columns: # seqnames ranges strand dna # <Rle> <IRanges> <Rle> <DNAStringSet> # [1] chrY 11001 * [C] # [2] chrY 11002 * [C] # [3] chrY 11003 * [A] # [4] chrY 11004 * [C] # [5] chrY 11005 * [C] # ... ... ... ... ... # [996] chrY 11996 * [C] # [997] chrY 11997 * [A] # [998] chrY 11998 * [A] # [999] chrY 11999 * [T] # [1000] chrY 12000 * [T] # ------- # seqinfo: 455 sequences (1 circular) from hg38 genome
the supplied GPos object is stored in the BSgenomeViews object as a GRanges instance:
class(v@granges) # [1] "GRanges" # attr(,"package") # [1] "GenomicRanges"
This unnecessary blows the size of the object so should be avoided.
> sessionInfo() R version 3.6.0 Patched (2019-05-02 r76454) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 16.04.5 LTS Matrix products: default BLAS: /home/hpages/R/R-3.6.r76454/lib/libRblas.so LAPACK: /home/hpages/R/R-3.6.r76454/lib/libRlapack.so 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] stats4 parallel stats graphics grDevices utils datasets [8] methods base other attached packages: [1] BSgenome.Hsapiens.UCSC.hg38_1.4.1 BSgenome_1.53.0 [3] rtracklayer_1.45.1 Biostrings_2.53.0 [5] XVector_0.25.0 GenomicRanges_1.37.7 [7] GenomeInfoDb_1.21.1 IRanges_2.19.5 [9] S4Vectors_0.23.3 BiocGenerics_0.31.2 loaded via a namespace (and not attached): [1] zlibbioc_1.31.0 GenomicAlignments_1.21.2 [3] BiocParallel_1.19.0 lattice_0.20-38 [5] tools_3.6.0 SummarizedExperiment_1.15.1 [7] grid_3.6.0 Biobase_2.45.0 [9] matrixStats_0.54.0 Matrix_1.2-17 [11] GenomeInfoDbData_1.2.1 bitops_1.0-6 [13] RCurl_1.95-4.12 DelayedArray_0.11.0 [15] compiler_3.6.0 Rsamtools_2.1.2 [17] XML_3.98-1.19
Even though the
BSgenomeViews()constructor accepts a GPos object:the supplied GPos object is stored in the BSgenomeViews object as a GRanges instance:
This unnecessary blows the size of the object so should be avoided.