I keep running into this issue no matter which arguments I try:

# using the colData argument
subsetSCECols(sce, colData = "condition == 'ctrl'")

>>  Error in S4Vectors::metadata(inSCE)$seurat$obj: $ operator is invalid for atomic vectors

# using the bool argument
subsetSCECols(sce, bool = colData(sce)$condition=="ctrl")

>> Error in S4Vectors::metadata(inSCE)$seurat$obj: $ operator is invalid for atomic vectors

I did check that everything is fine with my SingleCellExperiment object and its colData does have the 'condition' column with values like 'ctrl'.

Why is it checking seurat$obj here?

Session Info

R version 4.3.2 (2023-10-31) Platform: x86_64-conda-linux-gnu (64-bit) Running under: Ubuntu 22.04.3 LTS

Matrix products: default BLAS/LAPACK: /home/miniconda3/envs/scrna/lib/libopenblasp-r0.3.25.so; LAPACK version 3.11.0

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

other attached packages: [1] singleCellTK_2.12.0 DelayedArray_0.28.0
[3] SparseArray_1.2.3 S4Arrays_1.2.0
[5] abind_1.4-5 Matrix_1.6-5
[7] DESeq2_1.42.0 SingleCellExperiment_1.24.0 [9] SummarizedExperiment_1.32.0 Biobase_2.62.0
[11] GenomicRanges_1.54.1 GenomeInfoDb_1.38.5
[13] IRanges_2.36.0 S4Vectors_0.40.2
[15] BiocGenerics_0.48.1 MatrixGenerics_1.14.0
[17] matrixStats_1.2.0 glmGamPoi_1.14.0

loaded via a namespace (and not attached): [1] tidyselect_1.2.0 IRdisplay_1.1
[3] dplyr_1.1.4 R.utils_2.12.3
[5] bitops_1.0-7 fastmap_1.1.1
[7] RCurl_1.98-1.14 digest_0.6.34
[9] lifecycle_1.0.4 GSVAdata_1.38.0
[11] statmod_1.5.0 magrittr_2.0.3
[13] compiler_4.3.2 rlang_1.1.3
[15] tools_4.3.2 utf8_1.2.4
[17] dqrng_0.3.2 reticulate_1.34.0
[19] plyr_1.8.9 repr_1.1.6
[21] BiocParallel_1.36.0 HDF5Array_1.30.0
[23] pbdZMQ_0.3-11 R.oo_1.26.0
[25] grid_4.3.2 fansi_1.0.6
[27] beachmat_2.18.0 colorspace_2.1-0
[29] Rhdf5lib_1.24.1 edgeR_4.0.12
[31] ggplot2_3.4.4 scales_1.3.0
[33] cli_3.6.2 crayon_1.5.2
[35] generics_0.1.3 reshape2_1.4.4
[37] DelayedMatrixStats_1.24.0 scuttle_1.12.0
[39] rhdf5_2.46.1 stringr_1.5.1
[41] zlibbioc_1.48.0 parallel_4.3.2
[43] XVector_0.42.0 base64enc_0.1-3
[45] vctrs_0.6.5 jsonlite_1.8.8
[47] locfit_1.5-9.8 limma_3.58.1
[49] eds_1.4.0 glue_1.7.0
[51] DropletUtils_1.22.0 codetools_0.2-19
[53] stringi_1.8.3 gtable_0.3.4
[55] munsell_0.5.0 tibble_3.2.1
[57] pillar_1.9.0 htmltools_0.5.7
[59] rhdf5filters_1.14.1 IRkernel_1.3.2
[61] GenomeInfoDbData_1.2.11 R6_2.5.1
[63] sparseMatrixStats_1.14.0 evaluate_0.23
[65] lattice_0.22-5 R.methodsS3_1.8.2
[67] png_0.1-8 Rcpp_1.0.12
[69] uuid_1.2-0 pkgconfig_2.0.3

compbiomed / singleCellTK

subsetSCECols: S4Vectors::metadata(inSCE)$seurat$obj: $ operator is invalid for atomic vectors #743

Session Info