CreateChromatinAssay Error in .GetSeuratCompat() : could not find function ".GetSeuratCompat"

[dionne099]

Hi Seurat Team,

I am trying to create a chromatin assay from a feature matrix from fragment files of my data outputted by CellRanger ARC.

I generated the feature matrix as such: counts.FI <- FeatureMatrix( fragments = atac.frags.FI, features = gr.FI, cells = rownames(atac.frags.FI) )

where the features are a set GRanges from the ARC output bed file.

However, when I try to create a chromatin assay I get this error: FI_assay <- CreateChromatinAssay(counts.FI, fragments = atac.frags.FI) Warning: Feature names cannot have underscores ('_'), replacing with dashes ('-')Error in .GetSeuratCompat() : could not find function ".GetSeuratCompat"

Any advice on how to get around this error? I've tried uninstalling and re-installing V.4 Seurat and SeuratObject.

R version 4.2.1 (2022-06-23) Platform: x86_64-apple-darwin17.0 (64-bit) Running under: macOS Ventura 13.3.1

Matrix products: default LAPACK: /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRlapack.dylib

locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages: [1] stats4 stats graphics grDevices utils datasets [7] methods base

other attached packages: [1] RColorBrewer_1.1-3
[2] viridis_0.6.5
[3] viridisLite_0.4.2
[4] xlsx_0.6.5
[5] readxl_1.4.3
[6] patchwork_1.2.0
[7] BSgenome.Stuberosum.BUELL.Atlanticv3_1.0.0 [8] BSgenome_1.64.0
[9] rtracklayer_1.56.1
[10] Biostrings_2.64.1
[11] XVector_0.36.0
[12] GenomicRanges_1.48.0
[13] GenomeInfoDb_1.32.4
[14] IRanges_2.30.1
[15] S4Vectors_0.34.0
[16] BiocGenerics_0.42.0
[17] Signac_1.11.0
[18] SeuratObject_4.1.4
[19] Seurat_4.4.0
[20] lubridate_1.9.3
[21] forcats_1.0.0
[22] stringr_1.5.1
[23] dplyr_1.1.4
[24] purrr_1.0.2
[25] readr_2.1.5
[26] tidyr_1.3.1
[27] tibble_3.2.1
[28] ggplot2_3.4.4
[29] tidyverse_2.0.0
[30] edgeR_3.38.4
[31] limma_3.52.4

loaded via a namespace (and not attached): [1] spam_2.10-0 fastmatch_1.1-4
[3] plyr_1.8.9 igraph_1.5.1
[5] lazyeval_0.2.2 sp_2.1-3
[7] splines_4.2.1 BiocParallel_1.30.4
[9] listenv_0.9.1 scattermore_1.2
[11] digest_0.6.34 htmltools_0.5.7
[13] fansi_1.0.6 magrittr_2.0.3
[15] tensor_1.5 cluster_2.1.6
[17] ROCR_1.0-11 tzdb_0.4.0
[19] globals_0.16.2 matrixStats_1.2.0
[21] timechange_0.3.0 spatstat.sparse_3.0-3
[23] colorspace_2.1-0 ggrepel_0.9.5
[25] xfun_0.42 crayon_1.5.2
[27] RCurl_1.98-1.14 jsonlite_1.8.8
[29] progressr_0.14.0 spatstat.data_3.0-4
[31] survival_3.5-7 zoo_1.8-12
[33] glue_1.7.0 polyclip_1.10-6
[35] gtable_0.3.4 zlibbioc_1.42.0
[37] leiden_0.4.3.1 DelayedArray_0.22.0
[39] future.apply_1.11.1 ggbiplot_0.55
[41] abind_1.4-5 scales_1.3.0
[43] spatstat.random_3.2-2 miniUI_0.1.1.1
[45] Rcpp_1.0.12 xtable_1.8-4
[47] reticulate_1.35.0 dotCall64_1.1-1
[49] htmlwidgets_1.6.4 httr_1.4.7
[51] ellipsis_0.3.2 ica_1.0-3
[53] rJava_1.0-6 XML_3.99-0.16.1
[55] pkgconfig_2.0.3 uwot_0.1.16
[57] deldir_2.0-2 locfit_1.5-9.8
[59] utf8_1.2.4 tidyselect_1.2.0
[61] rlang_1.1.3 reshape2_1.4.4
[63] later_1.3.2 cellranger_1.1.0
[65] munsell_0.5.0 tools_4.2.1
[67] cli_3.6.2 generics_0.1.3
[69] ggridges_0.5.6 evaluate_0.23
[71] fastmap_1.1.1 yaml_2.3.8
[73] goftest_1.2-3 knitr_1.45
[75] fitdistrplus_1.1-11 RANN_2.6.1
[77] pbapply_1.7-2 future_1.33.1
[79] nlme_3.1-164 mime_0.12
[81] RcppRoll_0.3.0 compiler_4.2.1
[83] rstudioapi_0.15.0 plotly_4.10.4
[85] png_0.1-8 spatstat.utils_3.0-4
[87] stringi_1.8.3 lattice_0.22-5
[89] Matrix_1.6-5 vctrs_0.6.5
[91] pillar_1.9.0 lifecycle_1.0.4
[93] spatstat.geom_3.2-8 lmtest_0.9-40
[95] RcppAnnoy_0.0.22 data.table_1.15.0
[97] cowplot_1.1.3 bitops_1.0-7
[99] irlba_2.3.5.1 httpuv_1.6.14
[101] BiocIO_1.6.0 R6_2.5.1
[103] promises_1.2.1 KernSmooth_2.23-22
[105] gridExtra_2.3 parallelly_1.36.0
[107] codetools_0.2-19 MASS_7.3-60.0.1
[109] xlsxjars_0.6.1 SummarizedExperiment_1.26.1 [111] rjson_0.2.21 withr_3.0.0
[113] GenomicAlignments_1.32.1 sctransform_0.4.1
[115] Rsamtools_2.12.0 GenomeInfoDbData_1.2.8
[117] parallel_4.2.1 hms_1.1.3
[119] grid_4.2.1 rmarkdown_2.25
[121] MatrixGenerics_1.8.1 Rtsne_0.17
[123] spatstat.explore_3.2-6 Biobase_2.56.0
[125] shiny_1.8.0 restfulr_0.0.15

[mhkowalski]

Hello,

Please see this issue . The .GetSeuratCompat() function was released in SeuratObject version 5, so there might be a problem with multiple version installations.

[mhkowalski]

Hi,

We haven't heard back in a while, so I'm going to close this issue. Please feel free to re-open another issue if you continue to have problems, thank you!