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Solved. Needed to re-install dev version of Signac. Thanks. |
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Running the following code and getting this error when trying to call the ChromatinAssay object:
Error in h(simpleError(msg, call)) :
error in evaluating the argument 'x' in selecting a method for function 'genome': unable to find an inherited method for function 'seqinfo' for signature 'x = "ChromatinAssay"'
counts <- Matrix::readMM("path")
barcodes <- fread("path") #has all metadata information
peaks <- fread("path", sep = "\t", header = TRUE)
colnames(counts) <- barcodes$Barcodes
rownames(counts) <- peaks$Feature
assay <- CreateChromatinAssay(counts = counts, sep = c("", ""), genome = "hg19")
glimpse(assay)
assay ##shows error
SessionInfo():
R version 4.5.2 (2025-10-31 ucrt)
Platform: x86_64-w64-mingw32/x64
Running under: Windows 11 x64 (build 26100)
Matrix products: default
LAPACK version 3.12.1
locale:
[1] LC_COLLATE=English_United States.utf8
[2] LC_CTYPE=English_United States.utf8
[3] LC_MONETARY=English_United States.utf8
[4] LC_NUMERIC=C
[5] LC_TIME=English_United States.utf8
time zone: America/Los_Angeles
tzcode source: internal
attached base packages:
[1] stats4 stats graphics grDevices utils datasets methods
[8] base
other attached packages:
[1] BSgenome.Hsapiens.UCSC.hg19_1.4.3 BSgenome_1.76.0
[3] rtracklayer_1.68.0 BiocIO_1.18.0
[5] Biostrings_2.76.0 XVector_0.48.0
[7] data.table_1.17.8 AnnotationHub_3.16.1
[9] BiocFileCache_2.16.2 dbplyr_2.5.1
[11] GenomicRanges_1.60.0 GenomeInfoDb_1.44.3
[13] IRanges_2.42.0 S4Vectors_0.46.0
[15] BiocGenerics_0.54.1 generics_0.1.4
[17] lubridate_1.9.4 forcats_1.0.1
[19] stringr_1.6.0 dplyr_1.1.4
[21] purrr_1.2.0 readr_2.1.6
[23] tidyr_1.3.1 tibble_3.3.0
[25] ggplot2_4.0.1 tidyverse_2.0.0
[27] Signac_1.16.0 Seurat_5.3.1
[29] SeuratObject_5.2.0 sp_2.2-0
loaded via a namespace (and not attached):
[1] RcppAnnoy_0.0.22 splines_4.5.2
[3] later_1.4.4 bitops_1.0-9
[5] filelock_1.0.3 R.oo_1.27.1
[7] polyclip_1.10-7 XML_3.99-0.20
[9] fastDummies_1.7.5 lifecycle_1.0.4
[11] globals_0.18.0 lattice_0.22-7
[13] MASS_7.3-65 magrittr_2.0.4
[15] plotly_4.11.0 yaml_2.3.10
[17] httpuv_1.6.16 otel_0.2.0
[19] sctransform_0.4.2 spam_2.11-1
[21] spatstat.sparse_3.1-0 reticulate_1.44.1
[23] cowplot_1.2.0 pbapply_1.7-4
[25] DBI_1.2.3 RColorBrewer_1.1-3
[27] abind_1.4-8 Rtsne_0.17
[29] R.utils_2.13.0 RCurl_1.98-1.17
[31] rappdirs_0.3.3 GenomeInfoDbData_1.2.14
[33] ggrepel_0.9.6 irlba_2.3.5.1
[35] listenv_0.10.0 spatstat.utils_3.2-0
[37] goftest_1.2-3 RSpectra_0.16-2
[39] spatstat.random_3.4-2 fitdistrplus_1.2-4
[41] parallelly_1.45.1 DelayedArray_0.34.1
[43] codetools_0.2-20 RcppRoll_0.3.1
[45] tidyselect_1.2.1 UCSC.utils_1.4.0
[47] farver_2.1.2 matrixStats_1.5.0
[49] spatstat.explore_3.5-3 GenomicAlignments_1.44.0
[51] jsonlite_2.0.0 progressr_0.18.0
[53] ggridges_0.5.7 survival_3.8-3
[55] tools_4.5.2 ica_1.0-3
[57] Rcpp_1.1.0 glue_1.8.0
[59] SparseArray_1.8.1 gridExtra_2.3
[61] MatrixGenerics_1.20.0 withr_3.0.2
[63] BiocManager_1.30.27 fastmap_1.2.0
[65] digest_0.6.38 timechange_0.3.0
[67] R6_2.6.1 mime_0.13
[69] scattermore_1.2 tensor_1.5.1
[71] dichromat_2.0-0.1 spatstat.data_3.1-9
[73] RSQLite_2.4.4 R.methodsS3_1.8.2
[75] S4Arrays_1.8.1 httr_1.4.7
[77] htmlwidgets_1.6.4 uwot_0.2.4
[79] pkgconfig_2.0.3 gtable_0.3.6
[81] blob_1.2.4 lmtest_0.9-40
[83] S7_0.2.1 htmltools_0.5.8.1
[85] dotCall64_1.2 scales_1.4.0
[87] Biobase_2.68.0 png_0.1-8
[89] spatstat.univar_3.1-5 rjson_0.2.23
[91] tzdb_0.5.0 reshape2_1.4.5
[93] nlme_3.1-168 curl_7.0.0
[95] zoo_1.8-14 cachem_1.1.0
[97] BiocVersion_3.21.1 KernSmooth_2.23-26
[99] parallel_4.5.2 miniUI_0.1.2
[101] AnnotationDbi_1.70.0 restfulr_0.0.16
[103] pillar_1.11.1 grid_4.5.2
[105] vctrs_0.6.5 RANN_2.6.2
[107] promises_1.5.0 xtable_1.8-4
[109] cluster_2.1.8.1 cli_3.6.5
[111] compiler_4.5.2 Rsamtools_2.24.1
[113] rlang_1.1.6 crayon_1.5.3
[115] future.apply_1.20.0 plyr_1.8.9
[117] stringi_1.8.7 viridisLite_0.4.2
[119] deldir_2.0-4 BiocParallel_1.42.2
[121] lazyeval_0.2.2 spatstat.geom_3.6-0
[123] Matrix_1.7-4 RcppHNSW_0.6.0
[125] hms_1.1.4 patchwork_1.3.2
[127] bit64_4.6.0-1 future_1.68.0
[129] KEGGREST_1.48.1 shiny_1.11.1
[131] SummarizedExperiment_1.38.1 ROCR_1.0-11
[133] igraph_2.2.1 memoise_2.0.1
[135] fastmatch_1.1-6 bit_4.6.0
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