Open alkurowska opened 8 months ago
I am trying to covert my PFMatrixList into PWMatrixList
toPWM(my_PFMatrixList)
And I get the following error: Error in (function (classes, fdef, mtable) : unable to find an inherited method for function ‘bg’ for signature ‘"PFMatrix"’
> sessionInfo() R version 4.3.3 (2024-02-29) Platform: x86_64-conda-linux-gnu (64-bit) Running under: Rocky Linux 9.1 (Blue Onyx) Matrix products: default BLAS/LAPACK: /home/kurowsaa/miniconda3/envs/chromVAR_env/lib/libopenblasp-r0.3.26.so; LAPACK version 3.12.0 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/Riyadh tzcode source: system (glibc) attached base packages: [1] stats4 grid stats graphics grDevices utils datasets [8] methods base other attached packages: [1] BiocManager_1.30.22 lubridate_1.9.3 [3] forcats_1.0.0 stringr_1.5.1 [5] dplyr_1.1.4 purrr_1.0.2 [7] readr_2.1.5 tidyr_1.3.1 [9] tibble_3.2.1 ggplot2_3.5.0 [11] tidyverse_2.0.0 BSgenome.Hsapiens.UCSC.hg38_1.4.5 [13] BSgenome_1.70.1 rtracklayer_1.62.0 [15] BiocIO_1.12.0 Biostrings_2.70.1 [17] XVector_0.42.0 GenomicRanges_1.54.1 [19] GenomeInfoDb_1.38.1 IRanges_2.36.0 [21] S4Vectors_0.40.2 BiocGenerics_0.48.1 [23] TFBSTools_1.40.0 chromVAR_1.24.0 [25] motifmatchr_1.24.0 ComplexHeatmap_2.18.0 [27] learnMotifs_0.1.0 loaded via a namespace (and not attached): [1] RColorBrewer_1.1-3 jsonlite_1.8.8 [3] shape_1.4.6.1 magrittr_2.0.3 [5] GlobalOptions_0.1.2 zlibbioc_1.48.0 [7] vctrs_0.6.5 memoise_2.0.1 [9] Rsamtools_2.18.0 RCurl_1.98-1.14 [11] base64enc_0.1-3 htmltools_0.5.8 [13] S4Arrays_1.2.0 CNEr_1.38.0 [15] SparseArray_1.2.2 pracma_2.4.4 [17] htmlwidgets_1.6.4 plyr_1.8.9 [19] plotly_4.10.4 cachem_1.0.8 [21] GenomicAlignments_1.38.0 whisker_0.4.1 [23] mime_0.12 lifecycle_1.0.4 [25] iterators_1.0.14 pkgconfig_2.0.3 [27] Matrix_1.6-5 R6_2.5.1 [29] fastmap_1.1.1 GenomeInfoDbData_1.2.11 [31] MatrixGenerics_1.14.0 shiny_1.8.1 [33] clue_0.3-65 digest_0.6.35 [35] colorspace_2.1-0 TFMPvalue_0.0.9 [37] AnnotationDbi_1.64.1 RSQLite_2.3.4 [39] seqLogo_1.68.0 timechange_0.3.0 [41] fansi_1.0.6 tfruns_1.5.2 [43] httr_1.4.7 abind_1.4-5 [45] compiler_4.3.3 withr_3.0.0 [47] bit64_4.0.5 doParallel_1.0.17 [49] BiocParallel_1.36.0 DBI_1.2.2 [51] R.utils_2.12.3 tensorflow_2.15.0 [53] poweRlaw_0.80.0 DelayedArray_0.28.0 [55] rjson_0.2.21 gtools_3.9.5 [57] caTools_1.18.2 tools_4.3.3 [59] httpuv_1.6.15 ggseqlogo_0.2 [61] R.oo_1.26.0 glue_1.7.0 [63] restfulr_0.0.15 promises_1.2.1 [65] keras_2.13.0 cluster_2.1.6 [67] reshape2_1.4.4 generics_0.1.3 [69] gtable_0.3.4 tzdb_0.4.0 [71] R.methodsS3_1.8.2 data.table_1.15.2 [73] hms_1.1.3 utf8_1.2.4 [75] ggrepel_0.9.5 foreach_1.5.2 [77] pillar_1.9.0 later_1.3.2 [79] circlize_0.4.16 lattice_0.22-6 [81] bit_4.0.5 annotate_1.80.0 [83] tidyselect_1.2.1 DirichletMultinomial_1.44.0 [85] GO.db_3.18.0 miniUI_0.1.1.1 [87] SummarizedExperiment_1.32.0 Biobase_2.62.0 [89] matrixStats_1.2.0 DT_0.32 [91] stringi_1.8.3 lazyeval_0.2.2 [93] yaml_2.3.8 codetools_0.2-19 [95] cli_3.6.2 xtable_1.8-4 [97] reticulate_1.35.0 munsell_0.5.0 [99] Rcpp_1.0.12 zeallot_0.1.0 [101] png_0.1-8 XML_3.99-0.16.1 [103] parallel_4.3.3 blob_1.2.4 [105] bitops_1.0-7 viridisLite_0.4.2 [107] scales_1.3.0 crayon_1.5.2 [109] GetoptLong_1.0.5 rlang_1.1.3 [111] KEGGREST_1.42.0
I am trying to covert my PFMatrixList into PWMatrixList
toPWM(my_PFMatrixList)And I get the following error: Error in (function (classes, fdef, mtable) : unable to find an inherited method for function ‘bg’ for signature ‘"PFMatrix"’