RunChromVAR issue when selecting backgroud regions

[FFeiKong]

Hello,

When I run code below, I encounter some problem. My code: obj <- RunChromVAR( object = obj, genome = BSgenome.Hsapiens.UCSC.hg38, assay = "ATAC") Error: Error in seq.default(min(trans_norm_mat[, 1]), max(trans_norm_mat[, 1]), : 'from' must be a finite number

Could you please help me solve this? Thanks in advance.

sessionInfo R version 4.3.2 (2023-10-31) Platform: x86_64-conda-linux-gnu (64-bit) Running under: CentOS Linux 7 (Core)

Matrix products: default BLAS/LAPACK: /public/home/kongfanshu/.conda/envs/env_r432/lib/libopenblasp-r0.3.25.so; LAPACK version 3.11.0

Random number generation: RNG: L'Ecuyer-CMRG Normal: Inversion Sample: Rejection

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: Asia/Shanghai tzcode source: system (glibc)

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

other attached packages: [1] destiny_3.16.0 ggraph_2.1.0 [3] igraph_1.6.0 TFBSTools_1.40.0 [5] JASPAR2020_0.99.10 dplyr_1.1.4 [7] BSgenome.Hsapiens.UCSC.hg38_1.4.5 BSgenome_1.70.1 [9] rtracklayer_1.62.0 BiocIO_1.12.0 [11] Biostrings_2.70.1 XVector_0.42.0 [13] Nebulosa_1.12.0 patchwork_1.2.0 [15] harmony_1.2.0 scMEGA_1.0.2 [17] Signac_1.11.0 SeuratObject_4.1.4 [19] Seurat_4.3.0 rhdf5_2.46.1 [21] SummarizedExperiment_1.32.0 Biobase_2.62.0 [23] MatrixGenerics_1.14.0 Rcpp_1.0.12 [25] Matrix_1.6-5 GenomicRanges_1.54.1 [27] GenomeInfoDb_1.38.5 IRanges_2.36.0 [29] S4Vectors_0.40.2 BiocGenerics_0.48.1 [31] matrixStats_1.2.0 data.table_1.14.10 [33] stringr_1.5.1 plyr_1.8.9 [35] magrittr_2.0.3 ggplot2_3.4.4 [37] gtable_0.3.4 gtools_3.9.5 [39] gridExtra_2.3 ArchR_1.0.2

loaded via a namespace (and not attached): [1] spatstat.sparse_3.0-3 bitops_1.0-7 [3] DirichletMultinomial_1.44.0 httr_1.4.7 [5] RColorBrewer_1.1-3 tools_4.3.2 [7] sctransform_0.4.1 DT_0.31 [9] utf8_1.2.4 R6_2.5.1 [11] lazyeval_0.2.2 uwot_0.1.16 [13] rhdf5filters_1.14.1 withr_2.5.2 [15] sp_2.1-2 progressr_0.14.0 [17] cli_3.6.2 factoextra_1.0.7 [19] Cairo_1.6-2 spatstat.explore_3.2-5 [21] mvtnorm_1.2-4 robustbase_0.99-1 [23] spatstat.data_3.0-3 readr_2.1.5 [25] proxy_0.4-27 ggridges_0.5.5 [27] pbapply_1.7-2 Rsamtools_2.18.0 [29] R.utils_2.12.3 parallelly_1.36.0 [31] TTR_0.24.4 RSQLite_2.3.4 [33] generics_0.1.3 ica_1.0-3 [35] spatstat.random_3.2-2 car_3.1-2 [37] GO.db_3.18.0 fansi_1.0.6 [39] abind_1.4-5 R.methodsS3_1.8.2 [41] lifecycle_1.0.4 scatterplot3d_0.3-44 [43] yaml_2.3.8 carData_3.0-5 [45] SparseArray_1.2.3 Rtsne_0.17 [47] blob_1.2.4 promises_1.2.1 [49] crayon_1.5.2 miniUI_0.1.1.1 [51] lattice_0.22-5 cowplot_1.1.2 [53] annotate_1.80.0 KEGGREST_1.42.0 [55] pillar_1.9.0 rjson_0.2.21 [57] boot_1.3-28.1 future.apply_1.11.1 [59] codetools_0.2-19 fastmatch_1.1-4 [61] leiden_0.4.3.1 glue_1.7.0 [63] pcaMethods_1.94.0 vcd_1.4-12 [65] vctrs_0.6.5 png_0.1-8 [67] spam_2.10-0 poweRlaw_0.70.6 [69] cachem_1.0.8 ks_1.14.1 [71] S4Arrays_1.2.0 mime_0.12 [73] RcppEigen_0.3.3.9.4 tidygraph_1.3.0 [75] pracma_2.4.4 survival_3.5-7 [77] SingleCellExperiment_1.24.0 RcppRoll_0.3.0 [79] ellipsis_0.3.2 fitdistrplus_1.1-11 [81] ROCR_1.0-11 nlme_3.1-164 [83] xts_0.13.1 bit64_4.0.5 [85] RcppAnnoy_0.0.21 irlba_2.3.5.1 [87] KernSmooth_2.23-22 DBI_1.2.1 [89] colorspace_2.1-0 seqLogo_1.68.0 [91] nnet_7.3-19 tidyselect_1.2.0 [93] smoother_1.1 bit_4.0.5 [95] compiler_4.3.2 curl_5.2.0 [97] DelayedArray_0.28.0 plotly_4.10.3 [99] scales_1.3.0 caTools_1.18.2 [101] DEoptimR_1.1-3 lmtest_0.9-40 [103] hexbin_1.28.3 digest_0.6.34 [105] goftest_1.2-3 spatstat.utils_3.0-4 [107] htmltools_0.5.7 pkgconfig_2.0.3 [109] fastmap_1.1.1 rlang_1.1.3 [111] htmlwidgets_1.6.4 ggthemes_5.0.0 [113] shiny_1.8.0 farver_2.1.1 [115] zoo_1.8-12 jsonlite_1.8.8 [117] BiocParallel_1.36.0 mclust_6.0.1 [119] R.oo_1.25.0 RCurl_1.98-1.14 [121] GenomeInfoDbData_1.2.11 dotCall64_1.1-1 [123] Rhdf5lib_1.24.1 munsell_0.5.0 [125] viridis_0.6.4 reticulate_1.34.0 [127] stringi_1.8.3 zlibbioc_1.48.0 [129] MASS_7.3-60 parallel_4.3.2 [131] listenv_0.9.0 ggrepel_0.9.5 [133] CNEr_1.38.0 deldir_2.0-2 [135] graphlayouts_1.0.2 splines_4.3.2 [137] tensor_1.5 hms_1.1.3 [139] ranger_0.16.0 spatstat.geom_3.2-7 [141] RcppHNSW_0.5.0 reshape2_1.4.4 [143] TFMPvalue_0.0.9 XML_3.99-0.16 [145] laeken_0.5.2 chromVAR_1.24.0 [147] tzdb_0.4.0 tweenr_2.0.2 [149] httpuv_1.6.13 VIM_6.2.2 [151] RANN_2.6.1 tidyr_1.3.0 [153] purrr_1.0.2 polyclip_1.10-6 [155] future_1.33.1 scattermore_1.2 [157] ggforce_0.4.1 xtable_1.8-4 [159] restfulr_0.0.15 e1071_1.7-14 [161] RSpectra_0.16-1 later_1.3.2 [163] viridisLite_0.4.2 class_7.3-22 [165] tibble_3.2.1.9013 AnnotationDbi_1.64.1 [167] memoise_2.0.1 GenomicAlignments_1.38.1 [169] cluster_2.1.6 ggplot.multistats_1.0.0 [171] globals_0.16.2

[timoast]

Hi @FFeiKong, could you show the output of traceback() after getting the error message and the full code you're running?

[timoast]

Closing this as I haven't heard back, please reopen if you're still having issues and can provide the requested information