Error in LinkPeaks - Githubissues

I am trying to link gene peaks with their expression data while using the following code:

seurat_integrated <- LinkPeaks(seurat_integrated, peak.assay = "ATAC", expression.assay = "RNA", genes.use = c("Dpp9", "Fosl1"))

I keep getting the following error:

Testing 2 genes and 201368 peaks |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=11s Error: (converted from warning) 'as(, "dgTMatrix")' is deprecated. Use 'as(., "TsparseMatrix")' instead. See help("Deprecated") and help("Matrix-deprecated").

I would appreciate help in fixing the error. Below is my sessionInfo()

R version 4.3.1 (2023-06-16) Platform: x86_64-conda-linux-gnu (64-bit) Running under: Ubuntu 20.04.6 LTS

Matrix products: default BLAS/LAPACK: /localdisk/home/nnnadi/anaconda3/envs/r_4_3_1/lib/libopenblasp-r0.3.21.so; LAPACK version 3.9.0

locale: [1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8 [5] LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=en_GB.UTF-8 [7] LC_PAPER=en_GB.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C

time zone: Europe/London tzcode source: system (glibc)

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

other attached packages: [1] escape_1.12.0 Scillus_0.5.0 [3] DoMultiBarHeatmap_0.1.0 rlang_1.1.1 [5] BSgenome.Mmusculus.UCSC.mm10_1.4.3 BSgenome.Hsapiens.UCSC.hg38_1.4.5 [7] BSgenome_1.70.1 rtracklayer_1.62.0 [9] BiocIO_1.12.0 Biostrings_2.70.1 [11] XVector_0.42.0 EnsDb.Mmusculus.v79_2.99.0 [13] EnsDb.Hsapiens.v86_2.99.0 Signac_1.12.0 [15] paletteer_1.5.0 scCustomize_2.0.1 [17] ExploreModelMatrix_1.14.0 iSEE_2.14.0 [19] hexbin_1.28.3 ComplexHeatmap_2.18.0 [21] vsn_3.70.0 hgu95av2.db_3.13.0 [23] org.Mm.eg.db_3.18.0 fgsea_1.28.0 [25] msigdbr_7.5.1 readxl_1.4.3 [27] EnhancedVolcano_1.20.0 ggrepel_0.9.4 [29] data.table_1.14.8 loomR_0.2.1.9000 [31] hdf5r_1.3.8 R6_2.5.1 [33] RColorBrewer_1.1-3 DESeq2_1.42.0 [35] png_0.1-8 apeglm_1.24.0 [37] pheatmap_1.0.12 reshape2_1.4.4 [39] magrittr_2.0.3 edgeR_4.0.3 [41] limma_3.58.1 Matrix.utils_0.9.8 [43] Matrix_1.6-4 scater_1.30.1 [45] scuttle_1.12.0 reticulate_1.34.0 [47] ensembldb_2.26.0 AnnotationFilter_1.26.0 [49] GenomicFeatures_1.54.1 AnnotationHub_3.10.0 [51] BiocFileCache_2.10.1 dbplyr_2.3.4 [53] cowplot_1.1.1 scales_1.2.1 [55] RCurl_1.98-1.13 lubridate_1.9.3 [57] forcats_1.0.0 purrr_1.0.2 [59] readr_2.1.4 tidyverse_2.0.0 [61] SeuratDisk_0.0.0.9021 SeuratWrappers_0.3.2 [63] SeuratData_0.2.2.9001 Seurat_5.0.1 [65] SeuratObject_5.0.1 sp_2.1-1 [67] patchwork_1.1.3 multtest_2.58.0 [69] stringr_1.5.0 stringi_1.7.12 [71] tidyr_1.3.0 enrichplot_1.22.0 [73] clusterProfiler_4.10.0 devtools_2.4.5 [75] usethis_2.2.2 scmap_1.24.0 [77] gam_1.22-3 foreach_1.5.2 [79] clusterExperiment_2.22.0 zinbwave_1.24.0 [81] slingshot_2.10.0 TrajectoryUtils_1.10.0 [83] princurve_2.1.6 SCINA_1.2.0 [85] gplots_3.1.3 MASS_7.3-60 [87] MAST_1.28.0 SingleCellExperiment_1.24.0 [89] SummarizedExperiment_1.32.0 GenomicRanges_1.54.1 [91] GenomeInfoDb_1.38.1 MatrixGenerics_1.14.0 [93] matrixStats_1.2.0 ggmin_0.0.0.9000 [95] tibble_3.2.1 dplyr_1.1.3 [97] topGO_2.54.0 SparseM_1.81 [99] GO.db_3.18.0 graph_1.80.0 [101] dittoSeq_1.14.0 plotly_4.10.3 [103] ggplot2_3.4.4 viridis_0.6.4 [105] viridisLite_0.4.2 org.Hs.eg.db_3.18.0 [107] AnnotationDbi_1.64.1 IRanges_2.36.0 [109] S4Vectors_0.40.2 Biobase_2.62.0 [111] BiocGenerics_0.48.1

loaded via a namespace (and not attached): [1] igraph_1.6.0 ica_1.0-3 [3] rematch2_2.1.2 zlibbioc_1.48.0 [5] tidyselect_1.2.0 bit_4.0.5 [7] doParallel_1.0.17 clue_0.3-65 [9] lattice_0.22-5 rjson_0.2.21 [11] blob_1.2.4 urlchecker_1.0.1 [13] rngtools_1.5.2 S4Arrays_1.2.0 [15] parallel_4.3.1 RNeXML_2.4.11 [17] cli_3.6.1 ggplotify_0.1.2 [19] registry_0.5-1 rintrojs_0.3.3 [21] ProtGenerics_1.34.0 goftest_1.2-3 [23] kernlab_0.9-32 grr_0.9.5 [25] BiocNeighbors_1.20.0 uwot_0.1.16 [27] shadowtext_0.1.2 curl_5.1.0 [29] evaluate_0.22 mime_0.12 [31] tidytree_0.4.6 leiden_0.4.3.1 [33] howmany_0.3-1 backports_1.4.1 [35] XML_3.99-0.16 httpuv_1.6.11 [37] rappdirs_0.3.3 RcppRoll_0.3.0 [39] ggraph_2.1.0 DT_0.31 [41] sctransform_0.4.1 ggbeeswarm_0.7.2 [43] sessioninfo_1.2.2 DBI_1.1.3 [45] HDF5Array_1.30.0 jquerylib_0.1.4 [47] genefilter_1.84.0 withr_2.5.1 [49] emdbook_1.3.13 class_7.3-22 [51] lmtest_0.9-40 GSEABase_1.64.0 [53] bdsmatrix_1.3-6 tidygraph_1.2.3 [55] colourpicker_1.3.0 BiocManager_1.30.22 [57] htmlwidgets_1.6.4 fs_1.6.3 [59] biomaRt_2.58.0 SparseArray_1.2.2 [61] cellranger_1.1.0 sparsesvd_0.2-2 [63] rncl_0.8.7 annotate_1.80.0 [65] zoo_1.8-12 knitr_1.44 [67] docopt_0.7.1 timechange_0.2.0 [69] fansi_1.0.5 caTools_1.18.2 [71] ggtree_3.10.0 rhdf5_2.46.1 [73] R.oo_1.25.0 RSpectra_0.16-1 [75] irlba_2.3.5.1 ggrastr_1.0.2 [77] fastDummies_1.7.3 gridGraphics_0.5-1 [79] ellipsis_0.3.2 lazyeval_0.2.2 [81] yaml_2.3.7 ade4_1.7-22 [83] survival_3.5-7 scattermore_1.2 [85] BiocVersion_3.18.1 crayon_1.5.2 [87] RcppAnnoy_0.0.21 progressr_0.14.0 [89] tweenr_2.0.2 later_1.3.1 [91] GlobalOptions_0.1.2 ggridges_0.5.4 [93] codetools_0.2-19 profvis_0.3.8 [95] KEGGREST_1.42.0 shape_1.4.6 [97] bbmle_1.0.25.1 Rtsne_0.17 [99] Rsamtools_2.18.0 filelock_1.0.3 [101] pkgconfig_2.0.3 xml2_1.3.5 [103] GenomicAlignments_1.38.0 aplot_0.2.2 [105] spatstat.sparse_3.0-3 ape_5.7-1 [107] gridBase_0.4-7 xtable_1.8-4 [109] plyr_1.8.9 httr_1.4.7 [111] tools_4.3.1 globals_0.16.2 [113] pkgbuild_1.4.3 broom_1.0.5 [115] beeswarm_0.4.0 nlme_3.1-163 [117] affy_1.80.0 HDO.db_0.99.1 [119] shinyjs_2.1.0 digest_0.6.33 [121] numDeriv_2016.8-1.1 farver_2.1.1 [123] tzdb_0.4.0 yulab.utils_0.1.1 [125] glue_1.6.2 cachem_1.0.8 [127] polyclip_1.10-6 generics_0.1.3 [129] mvtnorm_1.2-4 presto_1.0.0 [131] parallelly_1.36.0 pkgload_1.3.3 [133] statmod_1.5.0 RcppHNSW_0.5.0 [135] ScaledMatrix_1.10.0 pbapply_1.7-2 [137] tcltk_4.3.1 spam_2.10-0 [139] gson_0.1.0 utf8_1.2.4 [141] graphlayouts_1.0.2 gtools_3.9.5 [143] preprocessCore_1.64.0 softImpute_1.4-1 [145] affyio_1.72.0 GSVA_1.50.0 [147] gridExtra_2.3 shiny_1.7.5.1 [149] GenomeInfoDbData_1.2.11 R.utils_2.12.3 [151] rhdf5filters_1.14.1 memoise_2.0.1 [153] rmarkdown_2.25 locfdr_1.1-8 [155] googleVis_0.7.1 R.methodsS3_1.8.2 [157] future_1.33.0 phylobase_0.8.10 [159] RANN_2.6.1 spatstat.data_3.0-3 [161] janitor_2.2.0 cluster_2.1.4 [163] spatstat.utils_3.0-4 hms_1.1.3 [165] fitdistrplus_1.1-11 munsell_0.5.0 [167] colorspace_2.1-0 shinyWidgets_0.8.0 [169] DelayedMatrixStats_1.24.0 sparseMatrixStats_1.14.0 [171] shinydashboard_0.7.2 dotCall64_1.1-1 [173] circlize_0.4.15 ggforce_0.4.1 [175] xfun_0.40 mgcv_1.9-0 [177] coda_0.19-4 e1071_1.7-13 [179] remotes_2.4.2.1 iterators_1.0.14 [181] abind_1.4-5 randomForest_4.7-1.1 [183] GOSemSim_2.28.0 interactiveDisplayBase_1.40.0 [185] treeio_1.26.0 Rhdf5lib_1.24.1 [187] bitops_1.0-7 promises_1.2.1 [189] scatterpie_0.2.1 RSQLite_2.3.4 [191] qvalue_2.34.0 qlcMatrix_0.9.7 [193] DelayedArray_0.28.0 proxy_0.4-27 [195] compiler_4.3.1 prettyunits_1.2.0 [197] beachmat_2.18.0 formattable_0.2.1 [199] listenv_0.9.0 Rcpp_1.0.11 [201] BiocSingular_1.18.0 tensor_1.5 [203] progress_1.2.2 UCell_2.6.2 [205] uuid_1.1-1 BiocParallel_1.36.0 [207] babelgene_22.9 spatstat.random_3.2-2 [209] fastmap_1.1.1 fastmatch_1.1-4 [211] vipor_0.4.5 ROCR_1.0-11 [213] rsvd_1.0.5 shinyAce_0.4.2 [215] gtable_0.3.4 KernSmooth_2.23-22 [217] miniUI_0.1.1.1 deldir_1.0-9 [219] htmltools_0.5.7 bit64_4.0.5 [221] ggprism_1.0.4 spatstat.explore_3.2-5 [223] lifecycle_1.0.3 restfulr_0.0.15 [225] sass_0.4.7 vctrs_0.6.4 [227] slam_0.1-50 snakecase_0.11.1 [229] spatstat.geom_3.2-7 DOSE_3.28.2 [231] NMF_0.26 ggfun_0.1.3 [233] future.apply_1.11.0 bslib_0.5.1 [235] pillar_1.9.0 locfit_1.5-9.8 [237] jsonlite_1.8.7 GetoptLong_1.0.5

stuart-lab / signac

Error in LinkPeaks #1778