Rstudio died when put more than three letters in subseting a SummarizedExperiment object
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Entering edit mode
Shuo GG • 0
@6c54ba5d
Last seen 8 weeks ago
China

se is my SummarizedExperiment object. The problem is, every time I want to use a function inside the se[ ] to do the subsetting, that breaks my Rstudio (specificly, it will not react to any commands or operations for a few minutes, though you can still input). And later I found that three letter in the square bracket is enough to make this happened. Like:

# se[aaa], se[row, ], se[1,aaa], se[1aaa, 1] or anything else, and then the Rstudio died
# below is my object and some of its content, hope it may help

> se
class: RangedSummarizedExperiment 
dim: 41786 22 
metadata(0):
assays(1): counts
rownames(41786): Xkr4 LOC105243853 ... TrnT TrnP
rowData names(3): ENTREZID product gbkey
colnames(22): GSM2545337 GSM2545338 ... GSM2545346 GSM2545347
colData names(12): title geo_accession ... Label Group

> head(colData(se), 1)
DataFrame with 1 row and 12 columns
                     title geo_accession     organism         age         sex   infection
               <character>   <character>  <character> <character> <character> <character>
GSM2545337 CNS_RNA-seq_11C    GSM2545337 Mus musculus     8 weeks      Female NonInfected
                strain        time      tissue     mouse         Label       Group
           <character> <character> <character> <integer>   <character>    <factor>
GSM2545337     C57BL/6        Day0  Cerebellum         9 Female_Day0_9 Female_Day0

> head(rowRanges(se), 1)
GRanges object with 1 range and 3 metadata columns:
       seqnames          ranges strand |    ENTREZID                product       gbkey
          <Rle>       <IRanges>  <Rle> | <character>            <character> <character>
  Xkr4        1 3670552-3671742      - |      497097 X Kell blood group p..        mRNA
  -------
  seqinfo: 90 sequences from an unspecified genome; no seqlengths

> sessionInfo( )
R version 4.4.1 (2024-06-14 ucrt)
Platform: x86_64-w64-mingw32/x64
Running under: Windows 11 x64 (build 22631)

Matrix products: default


locale:
[1] LC_COLLATE=Chinese (Simplified)_China.utf8  LC_CTYPE=Chinese (Simplified)_China.utf8   
[3] LC_MONETARY=Chinese (Simplified)_China.utf8 LC_NUMERIC=C                               
[5] LC_TIME=Chinese (Simplified)_China.utf8    

time zone: Asia/Shanghai
tzcode source: internal

attached base packages:
[1] grid      stats4    stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] iSEE_2.16.0                 SingleCellExperiment_1.26.0 hexbin_1.28.3              
 [4] RColorBrewer_1.1-3          ComplexHeatmap_2.20.0       ggplot2_3.5.1              
 [7] vsn_3.72.0                  DESeq2_1.44.0               SummarizedExperiment_1.34.0
[10] Biobase_2.64.0              GenomicRanges_1.56.1        GenomeInfoDb_1.40.1        
[13] IRanges_2.38.1              S4Vectors_0.42.1            BiocGenerics_0.50.0        
[16] MatrixGenerics_1.16.0       matrixStats_1.3.0          

loaded via a namespace (and not attached):
 [1] rlang_1.1.4             magrittr_2.0.3          shinydashboard_0.7.2   
 [4] clue_0.3-65             GetoptLong_1.0.5        compiler_4.4.1         
 [7] mgcv_1.9-1              png_0.1-8               vctrs_0.6.5            
[10] pkgconfig_2.0.3         shape_1.4.6.1           crayon_1.5.3           
[13] fastmap_1.2.0           XVector_0.44.0          labeling_0.4.3         
[16] utf8_1.2.4              promises_1.3.0          UCSC.utils_1.0.0       
[19] preprocessCore_1.66.0   shinyAce_0.4.2          cachem_1.1.0           
[22] zlibbioc_1.50.0         jsonlite_1.8.8          listviewer_4.0.0       
[25] later_1.3.2             DelayedArray_0.30.1     BiocParallel_1.38.0    
[28] parallel_4.4.1          cluster_2.1.6           R6_2.5.1               
[31] bslib_0.8.0             limma_3.60.4            jquerylib_0.1.4        
[34] Rcpp_1.0.13             iterators_1.0.14        httpuv_1.6.15          
[37] Matrix_1.7-0            splines_4.4.1           igraph_2.0.3           
[40] tidyselect_1.2.1        rstudioapi_0.16.0       abind_1.4-5            
[43] doParallel_1.0.17       codetools_0.2-20        affy_1.82.0            
[46] miniUI_0.1.1.1          lattice_0.22-6          tibble_3.2.1           
[49] shiny_1.9.1             withr_3.0.1             circlize_0.4.16        
[52] pillar_1.9.0            affyio_1.74.0           BiocManager_1.30.24    
[55] DT_0.33                 foreach_1.5.2           shinyjs_2.1.0          
[58] generics_0.1.3          munsell_0.5.1           scales_1.3.0           
[61] xtable_1.8-4            glue_1.7.0              tools_4.4.1            
[64] colourpicker_1.3.0      locfit_1.5-9.10         colorspace_2.1-1       
[67] nlme_3.1-166            GenomeInfoDbData_1.2.12 vipor_0.4.7            
[70] cli_3.6.3               fansi_1.0.6             viridisLite_0.4.2      
[73] S4Arrays_1.4.1          dplyr_1.1.4             gtable_0.3.5           
[76] rintrojs_0.3.4          sass_0.4.9              digest_0.6.37          
[79] SparseArray_1.4.8       ggrepel_0.9.5           farver_2.1.2           
[82] rjson_0.2.22            htmlwidgets_1.6.4       htmltools_0.5.8.1      
[85] lifecycle_1.0.4         httr_1.4.7              shinyWidgets_0.8.6     
[88] GlobalOptions_0.1.2     statmod_1.5.0           mime_0.12

Need some help! Thank you so much!

SummarizedExperiment • 356 views
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0
Entering edit mode
Shuo GG • 0
@6c54ba5d
Last seen 8 weeks ago
China

The problem is solved. It's because Rstudio try to autocomplete or suggest objects from the environment, even though I don't understand why it tries to search through my object. Anyway, if you encounter this question, you just need to disable autocomplete by: Tools -> Global Options -> Code -> Completion, and turn it off or set it to other mode.

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