Hi @timoast ,
I was running the ScRNA and the ATAC 10X multiomic data in below step showing me below error.
The preprocess step was:
annotation <- GetGRangesFromEnsDb(ensdb = EnsDb.Mmusculus.v79)
genome(annotation) <- "mm9"
seqlevelsStyle(annotation) <- "UCSC"
obj <- TSSEnrichment(obj)
Extracting TSS positions
Extracting fragments at TSSs
| | 0 % ~calculating Error in base::rowSums(x, na.rm = na.rm, dims = dims, ...) :
'x' must be an array of at least two dimensions
The version:
packageVersion('Signac')
[1] '1.3.0
sessionInfo()
R version 4.0.2 (2020-06-22)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)
Matrix products: default
BLAS: /share/nas1/Data/software/R/R-4.0.2/lib64/R/lib/libRblas.so
LAPACK: /share/nas1/Data/software/R/R-4.0.2/lib64/R/lib/libRlapack.so
locale:
[1] LC_CTYPE=zh_CN.UTF-8 LC_NUMERIC=C
[3] LC_TIME=zh_CN.UTF-8 LC_COLLATE=zh_CN.UTF-8
[5] LC_MONETARY=zh_CN.UTF-8 LC_MESSAGES=zh_CN.UTF-8
[7] LC_PAPER=zh_CN.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=zh_CN.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats4 parallel stats graphics grDevices utils datasets
[8] methods base
other attached packages:
[1] data.table_1.13.6 plyr_1.8.6
[3] dplyr_1.0.4 EnsDb.Mmusculus.v79_2.99.0
[5] BSgenome.Mmusculus.UCSC.mm10_1.4.0 BSgenome.Hsapiens.UCSC.hg19_1.4.3
[7] BSgenome.Hsapiens.UCSC.hg38_1.4.3 BSgenome_1.58.0
[9] rtracklayer_1.50.0 Biostrings_2.58.0
[11] XVector_0.30.0 cowplot_1.1.1
[13] ggplot2_3.3.3 EnsDb.Hsapiens.v86_2.99.0
[15] ensembldb_2.14.0 AnnotationFilter_1.14.0
[17] GenomicFeatures_1.42.1 AnnotationDbi_1.54.0
[19] Biobase_2.50.0 GenomicRanges_1.42.0
[21] GenomeInfoDb_1.26.2 IRanges_2.24.1
[23] S4Vectors_0.28.1 BiocGenerics_0.36.0
[25] Signac_1.3.0 SeuratObject_4.0.0
[27] Seurat_4.0.2
loaded via a namespace (and not attached):
[1] reticulate_1.18 tidyselect_1.1.0
[3] RSQLite_2.2.3 htmlwidgets_1.5.3
[5] grid_4.0.2 docopt_0.7.1
[7] BiocParallel_1.24.1 Rtsne_0.15
[9] munsell_0.5.0 codetools_0.2-16
[11] ica_1.0-2 future_1.21.0
[13] miniUI_0.1.1.1 withr_2.4.1
[15] colorspace_2.0-0 knitr_1.31
[17] rstudioapi_0.13 ROCR_1.0-11
[19] tensor_1.5 listenv_0.8.0
[21] MatrixGenerics_1.2.1 slam_0.1-48
[23] GenomeInfoDbData_1.2.4 polyclip_1.10-0
[25] bit64_4.0.5 farver_2.0.3
[27] parallelly_1.23.0 vctrs_0.3.6
[29] generics_0.1.0 xfun_0.21
[31] biovizBase_1.38.0 BiocFileCache_1.14.0
[33] lsa_0.73.2 ggseqlogo_0.1
[35] R6_2.5.0 bitops_1.0-6
[37] spatstat.utils_2.1-0 cachem_1.0.3
[39] DelayedArray_0.16.1 assertthat_0.2.1
[41] promises_1.2.0.1 scales_1.1.1
[43] nnet_7.3-14 gtable_0.3.0
[45] globals_0.14.0 goftest_1.2-2
[47] rlang_0.4.10 RcppRoll_0.3.0
[49] splines_4.0.2 lazyeval_0.2.2
[51] dichromat_2.0-0 checkmate_2.0.0
[53] spatstat.geom_2.1-0 reshape2_1.4.4
[55] abind_1.4-5 backports_1.2.1
[57] httpuv_1.5.5 Hmisc_4.4-2
[59] tools_4.0.2 ellipsis_0.3.1
[61] spatstat.core_2.1-2 RColorBrewer_1.1-2
[63] ggridges_0.5.3 Rcpp_1.0.6
[65] base64enc_0.1-3 progress_1.2.2
[67] zlibbioc_1.36.0 purrr_0.3.4
[69] RCurl_1.98-1.2 prettyunits_1.1.1
[71] rpart_4.1-15 openssl_1.4.3
[73] deldir_0.2-9 pbapply_1.4-3
[75] zoo_1.8-8 SummarizedExperiment_1.20.0
[77] ggrepel_0.9.1 cluster_2.1.0
[79] magrittr_2.0.1 scattermore_0.7
[81] lmtest_0.9-38 RANN_2.6.1
[83] SnowballC_0.7.0 ProtGenerics_1.22.0
[85] fitdistrplus_1.1-3 matrixStats_0.58.0
[87] hms_1.0.0 patchwork_1.1.1
[89] mime_0.9 xtable_1.8-4
[91] XML_3.99-0.5 jpeg_0.1-8.1
[93] sparsesvd_0.2 gridExtra_2.3
[95] compiler_4.0.2 biomaRt_2.46.3
[97] tibble_3.0.6 KernSmooth_2.23-17
[99] crayon_1.4.1 htmltools_0.5.1.1
[101] mgcv_1.8-31 later_1.1.0.1
[103] Formula_1.2-4 tidyr_1.1.2
[105] DBI_1.1.1 tweenr_1.0.1
[107] dbplyr_2.1.0 MASS_7.3-51.6
[109] rappdirs_0.3.3 Matrix_1.2-18
[111] igraph_1.2.6 pkgconfig_2.0.3
[113] GenomicAlignments_1.26.0 foreign_0.8-80
[115] plotly_4.9.3 spatstat.sparse_2.0-0
[117] xml2_1.3.2 VariantAnnotation_1.36.0
[119] stringr_1.4.0 digest_0.6.27
[121] sctransform_0.3.2 RcppAnnoy_0.0.18
[123] spatstat.data_2.1-0 leiden_0.3.7
[125] fastmatch_1.1-0 htmlTable_2.1.0
[127] uwot_0.1.10 curl_4.3
[129] shiny_1.6.0 Rsamtools_2.6.0
[131] lifecycle_0.2.0 nlme_3.1-148
[133] jsonlite_1.7.2 viridisLite_0.3.0
[135] askpass_1.1 pillar_1.4.7
[137] lattice_0.20-41 KEGGREST_1.30.1
[139] fastmap_1.1.0 httr_1.4.2
[141] survival_3.1-12 glue_1.4.2
[143] qlcMatrix_0.9.7 png_0.1-7
[145] bit_4.0.4 ggforce_0.3.2
[147] stringi_1.5.3 blob_1.2.1
[149] latticeExtra_0.6-29 memoise_2.0.0
[151] irlba_2.3.3 future.apply_1.7.0
So how can i fix this issue?
Any advice would be appreciated.
Best,
Hanhuihong
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