RunChromVAR Error - Githubissues

FFeiKong commented 9 months ago

@timoast Hi, tim, I try to run RunChromVAR in my code, and I encounter a problem you mentioned before. I try to solve it as you said in #1388 , but it seems like something goes wrong, could you please help me to solve it? Thank you very much!

Here's my code: obj <- RunChromVAR( object = obj, genome = BSgenome.Hsapiens.UCSC.hg38, assay = "ATAC" ) Error in .getOneSeqFromBSgenomeMultipleSequences(x, name, start, NA, width, : sequence GL000009.2 not found In addition: Warning message: In .merge_two_Seqinfo_objects(x, y) : Each of the 2 combined objects has sequence levels not in the other:

in 'x': chrM, chr1_GL383518v1_alt, chr1_GL383519v1_alt, chr1_GL383520v2_alt, chr1_KI270759v1_alt, chr1_KI270760v1_alt, chr1_KI270761v1_alt, chr1_KI270762v1_alt, chr1_KI270763v1_alt, chr1_KI270764v1_alt, chr1_KI270765v1_alt, chr1_KI270766v1_alt, chr1_KI270892v1_alt, chr2_GL383521v1_alt, chr2_GL383522v1_alt, chr2_GL582966v2_alt, chr2_KI270767v1_alt, chr2_KI270768v1_alt, chr2_KI270769v1_alt, chr2_KI270770v1_alt, chr2_KI270771v1_alt, chr2_KI270772v1_alt, chr2_KI270773v1_alt, chr2_KI270774v1_alt, chr2_KI270775v1_alt, chr2_KI270776v1_alt, chr2_KI270893v1_alt, chr2_KI270894v1_alt, chr3_GL383526v1_alt, chr3_JH636055v2_alt, chr3_KI270777v1_alt, chr3_KI270778v1_alt, chr3_KI270779v1_alt, chr3_KI270780v1_alt, chr3_KI270781v1_alt, chr3_KI270782v1_alt, chr3_KI270783v1_alt, chr3_KI270784v1_alt, chr3_KI270895v1_alt, chr3_KI270924v1_alt, chr3_KI270934v1_alt, chr3_KI270935v1_alt, chr3_KI270936v1_alt, chr3_KI270937v1_alt, chr4_GL000 [... truncated]

I try to solve this as below: features.keep <- as.character(seqnames(granges(obj))) %in% standardChromosomes(granges(obj)) and I get error: Error in h(simpleError(msg, call)) : error in evaluating the argument 'x' in selecting a method for function '%in%': error in evaluating the argument 'x' in selecting a method for function 'seqnames': unable to find an inherited method for function ‘granges’ for signature ‘"Assay"’

> obj An object of class Seurat 370986 features across 10303 samples within 2 assays Active assay: RNA (2298 features, 0 variable features) 1 other assay present: ATAC 5 dimensional reductions calculated: pca, harmony, umap, umap_harmony, dm

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] labeling_0.4.3 mvtnorm_1.2-4
[23] robustbase_0.99-1 spatstat.data_3.0-3
[25] readr_2.1.5 proxy_0.4-27
[27] ggridges_0.5.5 pbapply_1.7-2
[29] Rsamtools_2.18.0 R.utils_2.12.3
[31] parallelly_1.36.0 TTR_0.24.4
[33] RSQLite_2.3.4 generics_0.1.3
[35] ica_1.0-3 spatstat.random_3.2-2
[37] car_3.1-2 GO.db_3.18.0
[39] fansi_1.0.6 abind_1.4-5
[41] R.methodsS3_1.8.2 lifecycle_1.0.4
[43] scatterplot3d_0.3-44 yaml_2.3.8
[45] carData_3.0-5 SparseArray_1.2.3
[47] Rtsne_0.17 blob_1.2.4
[49] promises_1.2.1 crayon_1.5.2
[51] miniUI_0.1.1.1 lattice_0.22-5
[53] cowplot_1.1.2 annotate_1.80.0
[55] KEGGREST_1.42.0 pillar_1.9.0
[57] rjson_0.2.21 boot_1.3-28.1
[59] future.apply_1.11.1 codetools_0.2-19
[61] fastmatch_1.1-4 leiden_0.4.3.1
[63] glue_1.7.0 pcaMethods_1.94.0
[65] vcd_1.4-12 vctrs_0.6.5
[67] png_0.1-8 spam_2.10-0
[69] poweRlaw_0.70.6 cachem_1.0.8
[71] ks_1.14.1 S4Arrays_1.2.0
[73] mime_0.12 RcppEigen_0.3.3.9.4
[75] tidygraph_1.3.0 pracma_2.4.4
[77] survival_3.5-7 SingleCellExperiment_1.24.0 [79] RcppRoll_0.3.0 ellipsis_0.3.2
[81] fitdistrplus_1.1-11 ROCR_1.0-11
[83] nlme_3.1-164 xts_0.13.1
[85] bit64_4.0.5 RcppAnnoy_0.0.21
[87] irlba_2.3.5.1 KernSmooth_2.23-22
[89] DBI_1.2.1 colorspace_2.1-0
[91] seqLogo_1.68.0 nnet_7.3-19
[93] tidyselect_1.2.0 smoother_1.1
[95] bit_4.0.5 compiler_4.3.2
[97] curl_5.2.0 DelayedArray_0.28.0
[99] plotly_4.10.3 scales_1.3.0
[101] caTools_1.18.2 DEoptimR_1.1-3
[103] lmtest_0.9-40 hexbin_1.28.3
[105] nabor_0.5.0 digest_0.6.34
[107] goftest_1.2-3 spatstat.utils_3.0-4
[109] motifmatchr_1.24.0 htmltools_0.5.7
[111] pkgconfig_2.0.3 fastmap_1.1.1
[113] rlang_1.1.3 htmlwidgets_1.6.4
[115] ggthemes_5.0.0 shiny_1.8.0
[117] farver_2.1.1 zoo_1.8-12
[119] jsonlite_1.8.8 BiocParallel_1.36.0
[121] mclust_6.0.1 R.oo_1.25.0
[123] RCurl_1.98-1.14 GenomeInfoDbData_1.2.11
[125] dotCall64_1.1-1 Rhdf5lib_1.24.1
[127] munsell_0.5.0 viridis_0.6.4
[129] reticulate_1.34.0 stringi_1.8.3
[131] zlibbioc_1.48.0 MASS_7.3-60
[133] parallel_4.3.2 listenv_0.9.0
[135] ggrepel_0.9.5 CNEr_1.38.0
[137] deldir_2.0-2 graphlayouts_1.0.2
[139] splines_4.3.2 tensor_1.5
[141] hms_1.1.3 ranger_0.16.0
[143] spatstat.geom_3.2-7 RcppHNSW_0.5.0
[145] reshape2_1.4.4 TFMPvalue_0.0.9
[147] XML_3.99-0.16 laeken_0.5.2
[149] chromVAR_1.24.0 tzdb_0.4.0
[151] tweenr_2.0.2 httpuv_1.6.13
[153] VIM_6.2.2 RANN_2.6.1
[155] tidyr_1.3.0 purrr_1.0.2
[157] polyclip_1.10-6 future_1.33.1
[159] scattermore_1.2 ggforce_0.4.1
[161] xtable_1.8-4 restfulr_0.0.15
[163] e1071_1.7-14 RSpectra_0.16-1
[165] later_1.3.2 viridisLite_0.4.2
[167] class_7.3-22 tibble_3.2.1.9013
[169] AnnotationDbi_1.64.1 memoise_2.0.1
[171] GenomicAlignments_1.38.1 cluster_2.1.6
[173] ggplot.multistats_1.0.0 globals_0.16.2 `

Thanks in advance!

timoast commented 9 months ago

My guess is that the chromosome names are not matching in your object and the BSgenome object. Please check and reformat the BSgenome seqnames as necessary

FFeiKong commented 9 months ago

Thank you Tim, I have solved this problem by using code you offered in 2021 in #780 . Though I didn't know the reasons, code seems to be run. I will check what you proposed above, Thanks again. Best wishes, Kong

stuart-lab / signac

RunChromVAR Error #1641