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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!
