I have problems with the intiate_grn function.
my object looks like this
An object of class Seurat
117924 features across 1117 samples within 4 assays
Active assay: peaks (27383 features, 27225 variable features)
2 layers present: counts, data
3 other assays present: RNA, ATAC, SCT
3 dimensional reductions calculated: pca, lsi, umap
seurat.obj <- initiate_grn(seurat.obj,peak_assay = "peaks", rna_assay = "RNA",regions = "phastConsElements20Mammals.UCSC.hg38")
Error in (function (classes, fdef, mtable) :
unable to find an inherited method for function 'findOverlaps' for signature '"character", "GRanges"'
R version 4.3.0 (2023-04-21)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.4 LTS
I have problems with the intiate_grn function. my object looks like this An object of class Seurat 117924 features across 1117 samples within 4 assays Active assay: peaks (27383 features, 27225 variable features) 2 layers present: counts, data 3 other assays present: RNA, ATAC, SCT 3 dimensional reductions calculated: pca, lsi, umap
R version 4.3.0 (2023-04-21) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 20.04.4 LTS
Matrix products: default BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0 LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0
locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=de_DE.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=de_DE.UTF-8 LC_MESSAGES=en_US.UTF-8 LC_PAPER=de_DE.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=C
time zone: Europe/Busingen tzcode source: system (glibc)
attached base packages: [1] stats4 stats graphics grDevices utils datasets methods base
other attached packages: [1] TFBSTools_1.40.0 Pando_1.0.5 sceasy_0.0.7
[4] reticulate_1.34.0 lubridate_1.9.3 forcats_1.0.0
[7] stringr_1.5.1 dplyr_1.1.4 purrr_1.0.2
[10] readr_2.1.4 tidyr_1.3.0 tibble_3.2.1
[13] ggplot2_3.4.4 tidyverse_2.0.0 BSgenome.Hsapiens.UCSC.hg38_1.4.5 [16] BSgenome_1.70.1 rtracklayer_1.62.0 BiocIO_1.12.0
[19] Biostrings_2.70.1 XVector_0.42.0 EnsDb.Hsapiens.v86_2.99.0
[22] ensembldb_2.26.0 AnnotationFilter_1.26.0 GenomicFeatures_1.54.1
[25] AnnotationDbi_1.64.1 Biobase_2.62.0 GenomicRanges_1.54.1
[28] GenomeInfoDb_1.38.1 IRanges_2.36.0 S4Vectors_0.40.1
[31] BiocGenerics_0.48.1 Seurat_5.0.1 SeuratObject_5.0.1
[34] sp_2.1-1 Signac_1.12.9000
loaded via a namespace (and not attached): [1] ProtGenerics_1.34.0 matrixStats_1.1.0 spatstat.sparse_3.0-3 bitops_1.0-7
[5] DirichletMultinomial_1.44.0 httr_1.4.7 RColorBrewer_1.1-3 doParallel_1.0.17
[9] docopt_0.7.1 backports_1.4.1 tools_4.3.0 sctransform_0.4.1
[13] utf8_1.2.4 R6_2.5.1 lazyeval_0.2.2 uwot_0.1.16
[17] GetoptLong_1.0.5 withr_2.5.2 prettyunits_1.2.0 gridExtra_2.3
[21] progressr_0.14.0 cli_3.6.1 spatstat.explore_3.2-5 fastDummies_1.7.3
[25] slam_0.1-50 labeling_0.4.3 spatstat.data_3.0-3 ggridges_0.5.4
[29] pbapply_1.7-2 Rsamtools_2.18.0 foreign_0.8-85 R.utils_2.12.3
[33] dichromat_2.0-0.1 parallelly_1.36.0 maps_3.4.1.1 pals_1.8
[37] rstudioapi_0.15.0 RSQLite_2.3.3 generics_0.1.3 shape_1.4.6
[41] gtools_3.9.4 ica_1.0-3 spatstat.random_3.2-1 GO.db_3.18.0
[45] Matrix_1.6-3 fansi_1.0.5 abind_1.4-5 R.methodsS3_1.8.2
[49] lifecycle_1.0.4 yaml_2.3.7 SummarizedExperiment_1.32.0 glmGamPoi_1.14.0
[53] SparseArray_1.2.2 BiocFileCache_2.10.1 Rtsne_0.16 grid_4.3.0
[57] blob_1.2.4 promises_1.2.1 crayon_1.5.2 miniUI_0.1.1.1
[61] lattice_0.22-5 cowplot_1.1.1 annotate_1.80.0 mapproj_1.2.11
[65] KEGGREST_1.42.0 pillar_1.9.0 knitr_1.45 ComplexHeatmap_2.18.0
[69] rjson_0.2.21 future.apply_1.11.0 codetools_0.2-19 fastmatch_1.1-4
[73] leiden_0.4.3.1 glue_1.6.2 data.table_1.14.8 vctrs_0.6.4
[77] png_0.1-8 spam_2.10-0 poweRlaw_0.70.6 gtable_0.3.4
[81] cachem_1.0.8 xfun_0.41 S4Arrays_1.2.0 mime_0.12
[85] tidygraph_1.2.3 pracma_2.4.4 qlcMatrix_0.9.7 survival_3.5-7
[89] RcppRoll_0.3.0 iterators_1.0.14 ellipsis_0.3.2 fitdistrplus_1.1-11
[93] ROCR_1.0-11 nlme_3.1-163 bit64_4.0.5 progress_1.2.2
[97] filelock_1.0.2 RcppAnnoy_0.0.21 irlba_2.3.5.1 rpart_4.1.21
[101] KernSmooth_2.23-22 seqLogo_1.68.0 colorspace_2.1-0 DBI_1.1.3
[105] Hmisc_5.1-1 nnet_7.3-19 tidyselect_1.2.0 bit_4.0.5
[109] compiler_4.3.0 curl_5.1.0 htmlTable_2.4.2 xml2_1.3.5
[113] DelayedArray_0.28.0 plotly_4.10.3 caTools_1.18.2 checkmate_2.3.0
[117] scales_1.2.1 lmtest_0.9-40 rappdirs_0.3.3 digest_0.6.33
[121] goftest_1.2-3 spatstat.utils_3.0-4 sparsesvd_0.2-2 rmarkdown_2.25
[125] htmltools_0.5.7 pkgconfig_2.0.3 base64enc_0.1-3 sparseMatrixStats_1.14.0
[129] MatrixGenerics_1.14.0 dbplyr_2.4.0 fastmap_1.1.1 rlang_1.1.2
[133] GlobalOptions_0.1.2 htmlwidgets_1.6.2 DelayedMatrixStats_1.24.0 shiny_1.8.0
[137] farver_2.1.1 zoo_1.8-12 jsonlite_1.8.7 BiocParallel_1.36.0
[141] R.oo_1.25.0 VariantAnnotation_1.48.1 RCurl_1.98-1.13 magrittr_2.0.3
[145] Formula_1.2-5 GenomeInfoDbData_1.2.11 dotCall64_1.1-0 patchwork_1.1.3
[149] munsell_0.5.0 Rcpp_1.0.11 viridis_0.6.4 stringi_1.8.1
[153] ggraph_2.1.0 zlibbioc_1.48.0 MASS_7.3-60 plyr_1.8.9
[157] parallel_4.3.0 listenv_0.9.0 ggrepel_0.9.4 CNEr_1.38.0
[161] deldir_1.0-9 graphlayouts_1.0.2 splines_4.3.0 tensor_1.5
[165] hms_1.1.3 circlize_0.4.15 BPCells_0.1.0 igraph_1.4.3
[169] spatstat.geom_3.2-7 RcppHNSW_0.5.0 reshape2_1.4.4 biomaRt_2.58.0
[173] TFMPvalue_0.0.9 XML_3.99-0.15 evaluate_0.23 biovizBase_1.50.0
[177] tweenr_2.0.2 tzdb_0.4.0 foreach_1.5.2 httpuv_1.6.12
[181] RANN_2.6.1 polyclip_1.10-6 future_1.33.0 clue_0.3-65
[185] scattermore_1.2 ggforce_0.4.1 xtable_1.8-4 restfulr_0.0.15
[189] RSpectra_0.16-1 later_1.3.1 ggpointdensity_0.1.0 viridisLite_0.4.2
[193] memoise_2.0.1 GenomicAlignments_1.38.0 cluster_2.1.4 timechange_0.2.0
[197] globals_0.16.2