I found functions from Biostrings package in the Rgui and Rstudio returns very different results.
k70sv.ins.RMmasked is a DNAStringSet with 11967 strings. However, when simply print or show the length of k70sv.ins.RMmasker in Rstudio, it returns incorrect output (showing only 1 row and returns length of 1).
When the same command line runs in Rgui (please refer to the reply by me).
They output the correct length of DNAStringSet object and show the head and tail lines.
I don't know whether the problem is related to the colored visualization of DNAStringSet (grey background) in Rstudio interface.
Below is the sessoninfo and I am using a 1.3.1093 version Rstudio.
sessionInfo()
R version 4.0.3 (2020-10-10)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 18362)Matrix products: default
Random number generation:
RNG: Mersenne-Twister
Normal: Inversion
Sample: Roundinglocale:
[1] LC_COLLATE=Chinese (Simplified)_China.936 LC_CTYPE=Chinese (Simplified)_China.936
[3] LC_MONETARY=Chinese (Simplified)_China.936 LC_NUMERIC=C
[5] LC_TIME=Chinese (Simplified)_China.936attached base packages:
[1] grid stats4 parallel stats graphics grDevices utils datasets methods baseother attached packages:
[1] rGADEM_2.38.0 seqLogo_1.56.0 BSgenome_1.58.0 rtracklayer_1.49.5 GenomicRanges_1.42.0
[6] GenomeInfoDb_1.26.0 Biostrings_2.58.0 XVector_0.29.3 IRanges_2.24.0 S4Vectors_0.28.0
[11] BiocGenerics_0.36.0 TFBSTools_1.28.0loaded via a namespace (and not attached):
[1] MatrixGenerics_1.2.0 Biobase_2.50.0 httr_1.4.2
[4] bit64_4.0.5 R.utils_2.10.1 gtools_3.8.2
[7] blob_1.2.1 GenomeInfoDbData_1.2.4 Rsamtools_2.6.0
[10] DirichletMultinomial_1.32.0 pillar_1.4.6 RSQLite_2.2.1
[13] lattice_0.20-41 glue_1.4.2 digest_0.6.27
[16] colorspace_1.4-1 Matrix_1.2-18 R.oo_1.24.0
[19] plyr_1.8.6 XML_3.99-0.5 pkgconfig_2.0.3
[22] zlibbioc_1.35.0 purrr_0.3.4 xtable_1.8-4
[25] GO.db_3.12.0 scales_1.1.1 BiocParallel_1.24.0
[28] pracma_2.2.9 tibble_3.0.4 annotate_1.68.0
[31] KEGGREST_1.30.0 generics_0.0.2 ggplot2_3.3.2
[34] ellipsis_0.3.1 SummarizedExperiment_1.20.0 TFMPvalue_0.0.8
[37] magrittr_1.5 crayon_1.3.4 memoise_1.1.0
[40] poweRlaw_0.70.6 R.methodsS3_1.8.1 CNEr_1.26.0
[43] tools_4.0.3 hms_0.5.3 lifecycle_0.2.0
[46] matrixStats_0.57.0 stringr_1.4.0 munsell_0.5.0
[49] DelayedArray_0.16.0 AnnotationDbi_1.52.0 compiler_4.0.3
[52] caTools_1.18.0 rlang_0.4.8 RCurl_1.98-1.2
[55] bitops_1.0-6 gtable_0.3.0 DBI_1.1.0
[58] reshape2_1.4.4 R6_2.5.0 GenomicAlignments_1.26.0
[61] dplyr_1.0.2 bit_4.0.4 readr_1.4.0
[64] stringi_1.5.3 Rcpp_1.0.5 vctrs_0.3.4
[67] png_0.1-7 tidyselect_1.1.0