Entering edit mode
6 weeks ago
asap_student
•
0
Hello, I am new to Signac and R, and I have encountered an issue when using LinkPeaks . Here is my code:
# link peaks to genes
links <- LinkPeaks(
object = links,
peak.assay = "atac",
expression.assay = "rna",
)
I generated links following the Signac multimodal integration tutorial, but have used the CellRanger provided peak annotation rather than using the Signac tutorial pipeline. It has atac and rna assays, and I have added a GRanges object for the atac annotation, complete with the necessary metadata.
However when I attempt LinkPeaks , I get the following error:
Testing 20552 genes and 143835 peaks
Found gene coordinates for 14406 genes
Warning message in feature.weights * weights:
"longer object length is not a multiple of shorter object length"
...with the last two lines repeating over and over. Since this takes too long to run, I haven't been able to see the output. I apologies in advance that this may not be reproducible, but if anyone has encountered similar issues or has insights into a possible source for the problem, that would greatly help.
This is my session info (some omitted for privacy):
R version 4.3.1 (2023-06-16)
-
-
Matrix products: default
BLAS/LAPACK: - LAPACK version 3.12.0
-
attached base packages:
[1] stats4 stats graphics grDevices utils datasets methods
[8] base
other attached packages:
[1] BSgenome.Hsapiens.UCSC.hg38_1.4.5 BSgenome_1.70.2
[3] rtracklayer_1.62.0 BiocIO_1.12.0
[5] Biostrings_2.70.2 XVector_0.42.0
[7] EnsDb.Hsapiens.v86_2.99.0 ensembldb_2.26.0
[9] AnnotationFilter_1.26.0 GenomicFeatures_1.54.3
[11] AnnotationDbi_1.64.1 Biobase_2.62.0
[13] GenomicRanges_1.54.1 GenomeInfoDb_1.38.7
[15] IRanges_2.36.0 S4Vectors_0.40.2
[17] BiocGenerics_0.48.1 BiocManager_1.30.22
[19] SCENT_1.0.0 MuDataSeurat_0.0.0.9000
[21] Signac_1.12.0 Seurat_5.0.2
[23] SeuratObject_5.0.1 sp_2.1-3
loaded via a namespace (and not attached):
[1] ProtGenerics_1.34.0 matrixStats_1.2.0
[3] spatstat.sparse_3.0-3 bitops_1.0-7
[5] httr_1.4.7 RColorBrewer_1.1-3
[7] docopt_0.7.1 repr_1.1.6
[9] tools_4.3.1 sctransform_0.4.1
[11] backports_1.4.1 utf8_1.2.4
[13] R6_2.5.1 lazyeval_0.2.2
[15] uwot_0.1.16 withr_3.0.0
[17] prettyunits_1.2.0 gridExtra_2.3
[19] progressr_0.14.0 cli_3.6.2
[21] spatstat.explore_3.2-6 fastDummies_1.7.3
[23] slam_0.1-50 spatstat.data_3.0-4
[25] ggridges_0.5.6 pbapply_1.7-2
[27] Rsamtools_2.18.0 pbdZMQ_0.3-11
[29] foreign_0.8-86 R.utils_2.12.3
[31] parallelly_1.37.1 rstudioapi_0.15.0
[33] RSQLite_2.3.5 generics_0.1.3
[35] ica_1.0-3 spatstat.random_3.2-3
[37] dplyr_1.1.4 Matrix_1.6-5
[39] fansi_1.0.6 abind_1.4-5
[41] R.methodsS3_1.8.2 lifecycle_1.0.4
[43] yaml_2.3.8 SummarizedExperiment_1.32.0
[45] SparseArray_1.2.4 BiocFileCache_2.10.1
[47] Rtsne_0.17 grid_4.3.1
[49] blob_1.2.4 promises_1.2.1
[51] crayon_1.5.2 miniUI_0.1.1.1
[53] lattice_0.22-5 cowplot_1.1.3
[55] KEGGREST_1.42.0 pillar_1.9.0
[57] knitr_1.45 rjson_0.2.21
[59] boot_1.3-30 future.apply_1.11.1
[61] codetools_0.2-19 fastmatch_1.1-4
[63] leiden_0.4.3.1 glue_1.7.0
[65] data.table_1.15.2 vctrs_0.6.5
[67] png_0.1-8 spam_2.10-0
[69] gtable_0.3.4 cachem_1.0.8
[71] xfun_0.42 S4Arrays_1.2.1
[73] mime_0.12 qlcMatrix_0.9.7
[75] survival_3.5-8 RcppRoll_0.3.0
[77] ellipsis_0.3.2 fitdistrplus_1.1-11
[79] ROCR_1.0-11 nlme_3.1-164
[81] bit64_4.0.5 progress_1.2.3
[83] filelock_1.0.3 RcppAnnoy_0.0.22
[85] irlba_2.3.5.1 KernSmooth_2.23-22
[87] rpart_4.1.23 colorspace_2.1-0
[89] DBI_1.2.2 Hmisc_5.1-1
[91] nnet_7.3-19 tidyselect_1.2.0
[93] bit_4.0.5 compiler_4.3.1
[95] curl_5.2.1 htmlTable_2.4.2
[97] hdf5r_1.3.10 xml2_1.3.6
[99] DelayedArray_0.28.0 plotly_4.10.4
[101] checkmate_2.3.1 scales_1.3.0
[103] lmtest_0.9-40 rappdirs_0.3.3
[105] stringr_1.5.1 digest_0.6.34
[107] goftest_1.2-3 spatstat.utils_3.0-4
[109] minqa_1.2.6 sparsesvd_0.2-2
[111] rmarkdown_2.26 htmltools_0.5.7
[113] pkgconfig_2.0.3 base64enc_0.1-3
[115] lme4_1.1-35.1 MatrixGenerics_1.14.0
[117] dbplyr_2.4.0 fastmap_1.1.1
[119] rlang_1.1.3 htmlwidgets_1.6.4
[121] shiny_1.8.0 zoo_1.8-12
[123] jsonlite_1.8.8 BiocParallel_1.36.0
[125] R.oo_1.26.0 RCurl_1.98-1.14
[127] magrittr_2.0.3 Formula_1.2-5
[129] GenomeInfoDbData_1.2.11 dotCall64_1.1-1
[131] patchwork_1.2.0 IRkernel_1.3.2
[133] munsell_0.5.0 Rcpp_1.0.12
[135] reticulate_1.35.0 stringi_1.8.3
[137] zlibbioc_1.48.0 MASS_7.3-60.0.1
[139] plyr_1.8.9 parallel_4.3.1
[141] listenv_0.9.1 ggrepel_0.9.5
[143] deldir_2.0-4 IRdisplay_1.1
[145] splines_4.3.1 tensor_1.5
[147] hms_1.1.3 igraph_2.0.2
[149] uuid_1.2-0 spatstat.geom_3.2-9
[151] RcppHNSW_0.6.0 reshape2_1.4.4
[153] biomaRt_2.58.2 XML_3.99-0.16.1
[155] evaluate_0.23 nloptr_2.0.3
[157] httpuv_1.6.14 RANN_2.6.1
[159] tidyr_1.3.1 purrr_1.0.2
[161] polyclip_1.10-6 future_1.33.1
[163] scattermore_1.2 ggplot2_3.5.0
[165] xtable_1.8-4 restfulr_0.0.15
[167] RSpectra_0.16-1 later_1.3.2
[169] viridisLite_0.4.2 tibble_3.2.1
[171] memoise_2.0.1 GenomicAlignments_1.38.2
[173] cluster_2.1.6 globals_0.16.2
Thanks!
