Hello,
I am using MuSiC v1.0.0 and I'm getting the following error when running the music_prop() function:
Est.prop.Caris <- music_prop(bulk.mtx = merged_counts_1.mtx, sc.sce = combined.sce, clusters = 'predicted.id',
samples = 'orig.ident', verbose = F)
Error in h(simpleError(msg, call)) :
error in evaluating the argument 'i' in selecting a method for function '[': error in evaluating the argument 'x' in selecting a method for function 'rowSums': could not find function "counts"
Funnily enough, when I ran the exact same script a few weeks ago, the music_prop() function successfully output the results, but now rerunning the same exact script, this error is generated. Perhaps MuSiC or one of its dependencies was updated and no longer works on my original data? Any help would be greatly appreciated. I've also included the sessionInfo() below:
`attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] MuSiC_1.0.0 TOAST_1.18.0 quadprog_1.5-8 limma_3.60.6 EpiDISH_2.20.0 nnls_1.5
[7] Seurat_5.1.0 SeuratObject_5.0.2 sp_2.1-4 lubridate_1.9.3 forcats_1.0.0 stringr_1.5.1
[13] readr_2.1.5 tidyr_1.3.1 tibble_3.2.1 ggplot2_3.5.1 tidyverse_2.0.0 dplyr_1.1.4
[19] purrr_1.0.2
loaded via a namespace (and not attached):
[1] fs_1.6.5 matrixStats_1.4.1 spatstat.sparse_3.1-0 bitops_1.0-9
[5] enrichplot_1.24.2 EBImage_4.46.0 doParallel_1.0.17 HDO.db_0.99.1
[9] httr_1.4.7 RColorBrewer_1.1-3 tools_4.4.1 sctransform_0.4.1
[13] utf8_1.2.4 R6_2.5.1 lazyeval_0.2.2 uwot_0.2.2
[17] withr_3.0.2 GGally_2.2.1 gridExtra_2.3 progressr_0.14.0
[21] quantreg_5.98 cli_3.6.3 Biobase_2.64.0 spatstat.explore_3.3-1
[25] fastDummies_1.7.3 scatterpie_0.2.3 spatstat.data_3.1-2 proxy_0.4-27
[29] ggridges_0.5.6 pbapply_1.7-2 SPATAData_1.0.0 yulab.utils_0.1.5
[33] gson_0.1.0 DOSE_3.30.2 MCMCpack_1.7-0 parallelly_1.38.0
[37] rstudioapi_0.16.0 RSQLite_2.3.8 generics_0.1.3 gridGraphics_0.5-1
[41] ica_1.0-3 spatstat.random_3.3-1 GO.db_3.19.1 Matrix_1.7-0
[45] fansi_1.0.6 S4Vectors_0.42.1 abind_1.4-8 lifecycle_1.0.4
[49] SummarizedExperiment_1.34.0 qvalue_2.36.0 SparseArray_1.4.8 Rtsne_0.17
[53] grid_4.4.1 blob_1.2.4 promises_1.3.2 crayon_1.5.3
[57] miniUI_0.1.1.1 lattice_0.22-6 cowplot_1.1.3 KEGGREST_1.44.1
[61] pillar_1.9.0 knitr_1.49 fgsea_1.30.0 GenomicRanges_1.56.1
[65] corpcor_1.6.10 future.apply_1.11.2 codetools_0.2-20 fastmatch_1.1-4
[69] leiden_0.4.3.1 glue_1.8.0 ggfun_0.1.5 spatstat.univar_3.0-0
[73] data.table_1.16.2 vctrs_0.6.5 png_0.1-8 treeio_1.28.0
[77] spam_2.10-0 locfdr_1.1-8 gtable_0.3.6 cachem_1.1.0
[81] xfun_0.49 S4Arrays_1.4.1 mime_0.12 tidygraph_1.3.1
[85] coda_0.19-4.1 survival_3.7-0 SingleCellExperiment_1.26.0 iterators_1.0.14
[89] units_0.8-5 statmod_1.5.0 fitdistrplus_1.2-1 ROCR_1.0-11
[93] mcmc_0.9-8 nlme_3.1-165 ggtree_3.12.0 bit64_4.5.2
[97] RcppAnnoy_0.0.22 GenomeInfoDb_1.40.1 irlba_2.3.5.1 KernSmooth_2.23-24
[101] colorspace_2.1-1 BiocGenerics_0.50.0 DBI_1.2.3 SPATA2_3.0.1
[105] tidyselect_1.2.1 bit_4.5.0 compiler_4.4.1 SparseM_1.84-2
[109] DelayedArray_0.30.1 plotly_4.10.4 shadowtext_0.1.4 scales_1.3.0
[113] lmtest_0.9-40 tiff_0.1-12 digest_0.6.37 goftest_1.2-3
[117] fftwtools_0.9-11 spatstat.utils_3.0-5 XVector_0.44.0 htmltools_0.5.8.1
[121] pkgconfig_2.0.3 jpeg_0.1-10 MatrixGenerics_1.16.0 fastmap_1.2.0
[125] rlang_1.1.4 htmlwidgets_1.6.4 UCSC.utils_1.0.0 shiny_1.9.1
[129] farver_2.1.2 zoo_1.8-12 jsonlite_1.8.9 BiocParallel_1.38.0
[133] GOSemSim_2.30.0 RCurl_1.98-1.16 magrittr_2.0.3 GenomeInfoDbData_1.2.12
[137] ggplotify_0.1.2 dotCall64_1.1-1 patchwork_1.2.0 munsell_0.5.1
[141] Rcpp_1.0.13-1 ape_5.8 viridis_0.6.5 reticulate_1.38.0
[145] stringi_1.8.4 ggraph_2.2.1 zlibbioc_1.50.0 MASS_7.3-61
[149] plyr_1.8.9 ggstats_0.6.0 parallel_4.4.1 listenv_0.9.1
[153] ggrepel_0.9.6 deldir_2.0-4 Biostrings_2.72.1 graphlayouts_1.1.1
[157] splines_4.4.1 tensor_1.5 hms_1.1.3 locfit_1.5-9.10
[161] igraph_2.0.3 spatstat.geom_3.3-2 RcppHNSW_0.6.0 reshape2_1.4.4
[165] stats4_4.4.1 evaluate_1.0.1 foreach_1.5.2 tzdb_0.4.0
[169] tweenr_2.0.3 httpuv_1.6.15 MatrixModels_0.5-3 RANN_2.6.1
[173] polyclip_1.10-7 future_1.34.0 scattermore_1.2 ggforce_0.4.2
[177] xtable_1.8-4 e1071_1.7-16 RSpectra_0.16-2 tidytree_0.4.6
[181] later_1.4.1 class_7.3-22 viridisLite_0.4.2 clusterProfiler_4.12.2
[185] aplot_0.2.3 memoise_2.0.1 AnnotationDbi_1.66.0 IRanges_2.38.1
[189] cluster_2.1.6 timechange_0.3.0 globals_0.16.3 `
Thanks
Hello,
I am using MuSiC v1.0.0 and I'm getting the following error when running the music_prop() function:
Est.prop.Caris <- music_prop(bulk.mtx = merged_counts_1.mtx, sc.sce = combined.sce, clusters = 'predicted.id',
samples = 'orig.ident', verbose = F)
Error in h(simpleError(msg, call)) :
error in evaluating the argument 'i' in selecting a method for function '[': error in evaluating the argument 'x' in selecting a method for function 'rowSums': could not find function "counts"
Funnily enough, when I ran the exact same script a few weeks ago, the music_prop() function successfully output the results, but now rerunning the same exact script, this error is generated. Perhaps MuSiC or one of its dependencies was updated and no longer works on my original data? Any help would be greatly appreciated. I've also included the sessionInfo() below:
`attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] MuSiC_1.0.0 TOAST_1.18.0 quadprog_1.5-8 limma_3.60.6 EpiDISH_2.20.0 nnls_1.5
[7] Seurat_5.1.0 SeuratObject_5.0.2 sp_2.1-4 lubridate_1.9.3 forcats_1.0.0 stringr_1.5.1
[13] readr_2.1.5 tidyr_1.3.1 tibble_3.2.1 ggplot2_3.5.1 tidyverse_2.0.0 dplyr_1.1.4
[19] purrr_1.0.2
loaded via a namespace (and not attached):
[1] fs_1.6.5 matrixStats_1.4.1 spatstat.sparse_3.1-0 bitops_1.0-9
[5] enrichplot_1.24.2 EBImage_4.46.0 doParallel_1.0.17 HDO.db_0.99.1
[9] httr_1.4.7 RColorBrewer_1.1-3 tools_4.4.1 sctransform_0.4.1
[13] utf8_1.2.4 R6_2.5.1 lazyeval_0.2.2 uwot_0.2.2
[17] withr_3.0.2 GGally_2.2.1 gridExtra_2.3 progressr_0.14.0
[21] quantreg_5.98 cli_3.6.3 Biobase_2.64.0 spatstat.explore_3.3-1
[25] fastDummies_1.7.3 scatterpie_0.2.3 spatstat.data_3.1-2 proxy_0.4-27
[29] ggridges_0.5.6 pbapply_1.7-2 SPATAData_1.0.0 yulab.utils_0.1.5
[33] gson_0.1.0 DOSE_3.30.2 MCMCpack_1.7-0 parallelly_1.38.0
[37] rstudioapi_0.16.0 RSQLite_2.3.8 generics_0.1.3 gridGraphics_0.5-1
[41] ica_1.0-3 spatstat.random_3.3-1 GO.db_3.19.1 Matrix_1.7-0
[45] fansi_1.0.6 S4Vectors_0.42.1 abind_1.4-8 lifecycle_1.0.4
[49] SummarizedExperiment_1.34.0 qvalue_2.36.0 SparseArray_1.4.8 Rtsne_0.17
[53] grid_4.4.1 blob_1.2.4 promises_1.3.2 crayon_1.5.3
[57] miniUI_0.1.1.1 lattice_0.22-6 cowplot_1.1.3 KEGGREST_1.44.1
[61] pillar_1.9.0 knitr_1.49 fgsea_1.30.0 GenomicRanges_1.56.1
[65] corpcor_1.6.10 future.apply_1.11.2 codetools_0.2-20 fastmatch_1.1-4
[69] leiden_0.4.3.1 glue_1.8.0 ggfun_0.1.5 spatstat.univar_3.0-0
[73] data.table_1.16.2 vctrs_0.6.5 png_0.1-8 treeio_1.28.0
[77] spam_2.10-0 locfdr_1.1-8 gtable_0.3.6 cachem_1.1.0
[81] xfun_0.49 S4Arrays_1.4.1 mime_0.12 tidygraph_1.3.1
[85] coda_0.19-4.1 survival_3.7-0 SingleCellExperiment_1.26.0 iterators_1.0.14
[89] units_0.8-5 statmod_1.5.0 fitdistrplus_1.2-1 ROCR_1.0-11
[93] mcmc_0.9-8 nlme_3.1-165 ggtree_3.12.0 bit64_4.5.2
[97] RcppAnnoy_0.0.22 GenomeInfoDb_1.40.1 irlba_2.3.5.1 KernSmooth_2.23-24
[101] colorspace_2.1-1 BiocGenerics_0.50.0 DBI_1.2.3 SPATA2_3.0.1
[105] tidyselect_1.2.1 bit_4.5.0 compiler_4.4.1 SparseM_1.84-2
[109] DelayedArray_0.30.1 plotly_4.10.4 shadowtext_0.1.4 scales_1.3.0
[113] lmtest_0.9-40 tiff_0.1-12 digest_0.6.37 goftest_1.2-3
[117] fftwtools_0.9-11 spatstat.utils_3.0-5 XVector_0.44.0 htmltools_0.5.8.1
[121] pkgconfig_2.0.3 jpeg_0.1-10 MatrixGenerics_1.16.0 fastmap_1.2.0
[125] rlang_1.1.4 htmlwidgets_1.6.4 UCSC.utils_1.0.0 shiny_1.9.1
[129] farver_2.1.2 zoo_1.8-12 jsonlite_1.8.9 BiocParallel_1.38.0
[133] GOSemSim_2.30.0 RCurl_1.98-1.16 magrittr_2.0.3 GenomeInfoDbData_1.2.12
[137] ggplotify_0.1.2 dotCall64_1.1-1 patchwork_1.2.0 munsell_0.5.1
[141] Rcpp_1.0.13-1 ape_5.8 viridis_0.6.5 reticulate_1.38.0
[145] stringi_1.8.4 ggraph_2.2.1 zlibbioc_1.50.0 MASS_7.3-61
[149] plyr_1.8.9 ggstats_0.6.0 parallel_4.4.1 listenv_0.9.1
[153] ggrepel_0.9.6 deldir_2.0-4 Biostrings_2.72.1 graphlayouts_1.1.1
[157] splines_4.4.1 tensor_1.5 hms_1.1.3 locfit_1.5-9.10
[161] igraph_2.0.3 spatstat.geom_3.3-2 RcppHNSW_0.6.0 reshape2_1.4.4
[165] stats4_4.4.1 evaluate_1.0.1 foreach_1.5.2 tzdb_0.4.0
[169] tweenr_2.0.3 httpuv_1.6.15 MatrixModels_0.5-3 RANN_2.6.1
[173] polyclip_1.10-7 future_1.34.0 scattermore_1.2 ggforce_0.4.2
[177] xtable_1.8-4 e1071_1.7-16 RSpectra_0.16-2 tidytree_0.4.6
[181] later_1.4.1 class_7.3-22 viridisLite_0.4.2 clusterProfiler_4.12.2
[185] aplot_0.2.3 memoise_2.0.1 AnnotationDbi_1.66.0 IRanges_2.38.1
[189] cluster_2.1.6 timechange_0.3.0 globals_0.16.3 `
Thanks