Open bjstewart1 opened 7 months ago
infer_grn() is giving me this error Error in tf_g_cor[unique(tfs_use), , drop = F] : object of type 'S4' is not subsettable
infer_grn()
Error in tf_g_cor[unique(tfs_use), , drop = F] : object of type 'S4' is not subsettable
is this the problem? tf_g_cor <- as(sparse_cor(tf_x, g_x), 'generalMatrix')
tf_g_cor <- as(sparse_cor(tf_x, g_x), 'generalMatrix')
R version 4.3.2 (2023-10-31) Platform: x86_64-conda-linux-gnu (64-bit) Running under: Ubuntu 18.04.6 LTS Matrix products: default BLAS/LAPACK: /nfs/team297/bs16/tools/conda_envs/r_pando/lib/libopenblasp-r0.3.24.so; LAPACK version 3.11.0 locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C time zone: Europe/London tzcode source: system (glibc) attached base packages: [1] stats4 stats graphics grDevices utils datasets methods [8] base other attached packages: [1] MatrixGenerics_1.14.0 matrixStats_1.1.0 [3] BSgenome.Hsapiens.UCSC.hg38_1.4.5 BSgenome_1.70.1 [5] BiocIO_1.12.0 Biostrings_2.70.1 [7] XVector_0.42.0 dplyr_1.1.3 [9] rtracklayer_1.62.0 EnsDb.Hsapiens.v86_2.99.0 [11] ensembldb_2.26.0 AnnotationFilter_1.26.0 [13] GenomicFeatures_1.54.1 AnnotationDbi_1.64.1 [15] Biobase_2.62.0 GenomicRanges_1.54.1 [17] GenomeInfoDb_1.38.1 IRanges_2.36.0 [19] S4Vectors_0.40.1 BiocGenerics_0.48.1 [21] SeuratObject_4.1.4 Seurat_4.3.0 [23] Signac_1.11.0 Pando_1.0.5 [25] reticulate_1.34.0 loaded via a namespace (and not attached): [1] ProtGenerics_1.34.0 spatstat.sparse_3.0-3 [3] bitops_1.0-7 DirichletMultinomial_1.44.0 [5] TFBSTools_1.40.0 httr_1.4.7 [7] RColorBrewer_1.1-3 tools_4.3.2 [9] sctransform_0.4.1 utf8_1.2.4 [11] R6_2.5.1 lazyeval_0.2.2 [13] uwot_0.1.16 withr_2.5.2 [15] sp_2.1-1 prettyunits_1.2.0 [17] gridExtra_2.3 progressr_0.14.0 [19] cli_3.6.1 spatstat.explore_3.2-5 [21] spatstat.data_3.0-3 readr_2.1.4 [23] ggridges_0.5.4 pbapply_1.7-2 [25] Rsamtools_2.18.0 R.utils_2.12.2 [27] dichromat_2.0-0.1 parallelly_1.36.0 [29] maps_3.4.1.1 RSQLite_2.3.3 [31] pals_1.8 generics_0.1.3 [33] gtools_3.9.4 ica_1.0-3 [35] spatstat.random_3.2-1 GO.db_3.18.0 [37] Matrix_1.6-3 fansi_1.0.5 [39] abind_1.4-5 R.methodsS3_1.8.2 [41] lifecycle_1.0.4 yaml_2.3.7 [43] SummarizedExperiment_1.32.0 SparseArray_1.2.2 [45] BiocFileCache_2.10.1 Rtsne_0.16 [47] grid_4.3.2 blob_1.2.4 [49] promises_1.2.1 crayon_1.5.2 [51] miniUI_0.1.1.1 lattice_0.22-5 [53] cowplot_1.1.1 annotate_1.80.0 [55] KEGGREST_1.42.0 mapproj_1.2.11 [57] pillar_1.9.0 rjson_0.2.21 [59] future.apply_1.11.0 codetools_0.2-19 [61] fastmatch_1.1-4 leiden_0.4.3 [63] glue_1.6.2 data.table_1.14.8 [65] vctrs_0.6.4 png_0.1-8 [67] spam_2.10-0 gtable_0.3.4 [69] poweRlaw_0.70.6 cachem_1.0.8 [71] S4Arrays_1.2.0 mime_0.12 [73] tidygraph_1.2.3 pracma_2.4.4 [75] survival_3.5-7 RcppRoll_0.3.0 [77] ellipsis_0.3.2 fitdistrplus_1.1-11 [79] ROCR_1.0-11 nlme_3.1-163 [81] bit64_4.0.5 progress_1.2.2 [83] filelock_1.0.2 RcppAnnoy_0.0.21 [85] irlba_2.3.5.1 KernSmooth_2.23-22 [87] colorspace_2.1-0 seqLogo_1.68.0 [89] DBI_1.1.3 tidyselect_1.2.0 [91] bit_4.0.5 compiler_4.3.2 [93] curl_5.1.0 xml2_1.3.5 [95] DelayedArray_0.28.0 plotly_4.10.3 [97] scales_1.2.1 caTools_1.18.2 [99] lmtest_0.9-40 rappdirs_0.3.3 [101] stringr_1.5.1 digest_0.6.33 [103] goftest_1.2-3 spatstat.utils_3.0-4 [105] motifmatchr_1.24.0 htmltools_0.5.7 [107] pkgconfig_2.0.3 sparseMatrixStats_1.14.0 [109] dbplyr_2.4.0 fastmap_1.1.1 [111] rlang_1.1.2 htmlwidgets_1.6.2 [113] shiny_1.7.5.1 farver_2.1.1 [115] zoo_1.8-12 jsonlite_1.8.7 [117] BiocParallel_1.36.0 R.oo_1.25.0 [119] RCurl_1.98-1.13 magrittr_2.0.3 [121] GenomeInfoDbData_1.2.11 dotCall64_1.1-0 [123] patchwork_1.1.3 munsell_0.5.0 [125] Rcpp_1.0.11 viridis_0.6.4 [127] stringi_1.8.1 ggraph_2.1.0 [129] zlibbioc_1.48.0 MASS_7.3-60 [131] plyr_1.8.9 parallel_4.3.2 [133] listenv_0.9.0 ggrepel_0.9.4 [135] deldir_1.0-9 CNEr_1.38.0 [137] graphlayouts_1.0.2 splines_4.3.2 [139] tensor_1.5 hms_1.1.3 [141] igraph_1.5.1 spatstat.geom_3.2-7 [143] reshape2_1.4.4 biomaRt_2.58.0 [145] TFMPvalue_0.0.9 XML_3.99-0.15 [147] tzdb_0.4.0 tweenr_2.0.2 [149] httpuv_1.6.12 grr_0.9.5 [151] RANN_2.6.1 tidyr_1.3.0 [153] purrr_1.0.2 polyclip_1.10-6 [155] future_1.33.0 scattermore_1.2 [157] ggplot2_3.4.4 ggforce_0.4.1 [159] xtable_1.8-4 restfulr_0.0.15 [161] later_1.3.1 viridisLite_0.4.2 [163] ggpointdensity_0.1.0 tibble_3.2.1 [165] memoise_2.0.1 GenomicAlignments_1.38.0 [167] cluster_2.1.4 globals_0.16.2
infer_grn()
is giving me this errorError in tf_g_cor[unique(tfs_use), , drop = F] : object of type 'S4' is not subsettable
is this the problem?
tf_g_cor <- as(sparse_cor(tf_x, g_x), 'generalMatrix')