Unable to fetch peakxmotif and motifxTF using getObjectsForModelFit function

[Ajaingithub]

Dear,

Thanks for providing TRIPOD. I am following the vignette for data preprocessing. While running getObjectsForModelFit on the object provided i.e. pbmc.chromvar.rds. I am not able to get desired result in the peakxmotif and motifxTF.

I have loaded the RDS downloaded from the site provided on the vignette. Then ran the following command.

tripod_pbmc <- getObjectsForModelFit(object = pbmc, chr = paste0("chr", 1:22),convert = TRUE)

I am not getting any error but the output for motifxTF is empty

tripod_pbmc$motifxTF
motif TF

while for peakxmotif I am getting no motif with the peaks.

head(tripod_pbmc$peakxmotif)
6 x 0 sparse Matrix of class "dgCMatrix"

chr1-10109-10357 chr1-180730-181630 chr1-191491-191736 chr1-267816-268196 chr1-586028-586373 chr1-629721-630172

Is there anything I am doing wrong. Please help.

Please let me know if you need more information.

sessionInfo()
R version 4.0.5 (2021-03-31)
Platform: x86_64-conda-linux-gnu (64-bit)
Running under: Red Hat Enterprise Linux Server 7.9 (Maipo)

locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=C [4] LC_COLLATE=C LC_MONETARY=C LC_MESSAGES=C [7] LC_PAPER=C LC_NAME=C LC_ADDRESS=C [10] LC_TELEPHONE=C LC_MEASUREMENT=C LC_IDENTIFICATION=C

attached base packages: [1] parallel stats4 stats graphics grDevices utils datasets [8] methods base

other attached packages: [1] motifmatchr_1.12.0 TFBSTools_1.28.0 [3] JASPAR2020_0.99.10 chromVAR_1.12.0 [5] BSgenome.Hsapiens.UCSC.hg38_1.4.3 BSgenome_1.58.0 [7] rtracklayer_1.50.0 Biostrings_2.58.0 [9] XVector_0.30.0 EnsDb.Hsapiens.v86_2.99.0 [11] ensembldb_2.14.1 AnnotationFilter_1.14.0 [13] GenomicFeatures_1.42.3 AnnotationDbi_1.52.0 [15] Biobase_2.50.0 GenomicRanges_1.42.0 [17] GenomeInfoDb_1.26.7 IRanges_2.24.1 [19] S4Vectors_0.28.1 BiocGenerics_0.36.1 [21] Signac_1.6.0 SeuratDisk_0.0.0.9019 [23] sp_1.5-0 SeuratObject_4.1.2 [25] Seurat_4.2.0 patchwork_1.1.2 [27] ggplot2_3.3.6 dplyr_1.0.10 [29] BiocParallel_1.24.1 TRIPOD_0.0.1

loaded via a namespace (and not attached): [1] rappdirs_0.3.3 SnowballC_0.7.0 [3] scattermore_0.8 R.methodsS3_1.8.2 [5] tidyr_1.2.1 bit64_4.0.5 [7] knitr_1.40 R.utils_2.12.0 [9] irlba_2.3.5 DelayedArray_0.16.3 [11] data.table_1.14.2 rpart_4.1.16 [13] KEGGREST_1.30.1 RCurl_1.98-1.8 [15] generics_0.1.3 cowplot_1.1.1 [17] RSQLite_2.2.17 RANN_2.6.1 [19] future_1.28.0 tzdb_0.3.0 [21] bit_4.0.4 spatstat.data_2.2-0 [23] xml2_1.3.3 httpuv_1.6.6 [25] SummarizedExperiment_1.20.0 assertthat_0.2.1 [27] DirichletMultinomial_1.32.0 viridis_0.6.2 [29] xfun_0.33 hms_1.1.2 [31] promises_1.2.0.1 fansi_1.0.3 [33] progress_1.2.2 caTools_1.18.2 [35] dendextend_1.16.0 dbplyr_2.2.1 [37] igraph_1.3.5 DBI_1.1.3 [39] htmlwidgets_1.5.4 sparsesvd_0.2-1 [41] spatstat.geom_2.4-0 purrr_0.3.4 [43] ellipsis_0.3.2 backports_1.4.1 [45] annotate_1.68.0 biomaRt_2.46.3 [47] deldir_1.0-6 MatrixGenerics_1.2.1 [49] vctrs_0.4.2 ROCR_1.0-11 [51] abind_1.4-5 cachem_1.0.6 [53] withr_2.5.0 ggforce_0.4.0 [55] progressr_0.11.0 checkmate_2.1.0 [57] sctransform_0.3.5 GenomicAlignments_1.26.0 [59] prettyunits_1.1.1 goftest_1.2-3 [61] cluster_2.1.4 seqLogo_1.56.0 [63] lazyeval_0.2.2 crayon_1.5.2 [65] hdf5r_1.3.6 glmnet_4.1-4 [67] pkgconfig_2.0.3 slam_0.1-50 [69] tweenr_2.0.2 nlme_3.1-159 [71] ProtGenerics_1.22.0 nnet_7.3-18 [73] rlang_1.0.6 globals_0.16.1 [75] lifecycle_1.0.2 miniUI_0.1.1.1 [77] BiocFileCache_1.14.0 polyclip_1.10-0 [79] matrixStats_0.62.0 lmtest_0.9-40 [81] Matrix_1.5-1 ggseqlogo_0.1 [83] carData_3.0-5 zoo_1.8-11 [85] base64enc_0.1-3 ggridges_0.5.4 [87] png_0.1-7 viridisLite_0.4.1 [89] bitops_1.0-7 R.oo_1.25.0 [91] KernSmooth_2.23-20 blob_1.2.3 [93] shape_1.4.6 stringr_1.4.1 [95] parallelly_1.32.1 spatstat.random_2.2-0 [97] readr_2.1.2 jpeg_0.1-9 [99] CNEr_1.26.0 scales_1.2.1 [101] memoise_2.0.1 magrittr_2.0.3 [103] plyr_1.8.7 ica_1.0-3 [105] zlibbioc_1.36.0 compiler_4.0.5 [107] RColorBrewer_1.1-3 fitdistrplus_1.1-8 [109] Rsamtools_2.6.0 cli_3.4.1 [111] listenv_0.8.0 pbapply_1.5-0 [113] htmlTable_2.4.1 Formula_1.2-4 [115] MASS_7.3-58.1 mgcv_1.8-40 [117] tidyselect_1.1.2 stringi_1.7.6 [119] askpass_1.1 latticeExtra_0.6-30 [121] ggrepel_0.9.1 grid_4.0.5 [123] fastmatch_1.1-3 tools_4.0.5 [125] future.apply_1.9.1 rstudioapi_0.14 [127] TFMPvalue_0.0.8 foreach_1.5.2 [129] foreign_0.8-83 lsa_0.73.3 [131] gridExtra_2.3 farver_2.1.1 [133] Rtsne_0.16 digest_0.6.29 [135] rgeos_0.5-9 pracma_2.4.2 [137] FNN_1.1.3.1 shiny_1.7.2 [139] qlcMatrix_0.9.7 nortest_1.0-4 [141] Rcpp_1.0.9 car_3.1-0 [143] later_1.3.0 RcppAnnoy_0.0.19 [145] httr_1.4.4 colorspace_2.0-3 [147] XML_3.99-0.10 tensor_1.5 [149] reticulate_1.26 splines_4.0.5 [151] uwot_0.1.14 RcppRoll_0.3.0 [153] spatstat.utils_2.3-1 plotly_4.10.0 [155] xtable_1.8-4 poweRlaw_0.70.6 [157] jsonlite_1.8.0 R6_2.5.1 [159] Hmisc_4.7-1 pillar_1.8.1 [161] htmltools_0.5.3 mime_0.12 [163] glue_1.6.2 fastmap_1.1.0 [165] olsrr_0.5.3 DT_0.25 [167] codetools_0.2-18 utf8_1.2.2 [169] lattice_0.20-45 spatstat.sparse_2.1-1 [171] tibble_3.1.8 curl_4.3.2 [173] leiden_0.4.3 gtools_3.9.3 [175] GO.db_3.12.1 openssl_2.0.3 [177] interp_1.1-3 survival_3.4-0 [179] nbpMatching_1.5.1 docopt_0.7.1 [181] munsell_0.5.0 GenomeInfoDbData_1.2.4 [183] iterators_1.0.14 reshape2_1.4.4 [185] gtable_0.3.1 spatstat.core_2.4-4

Thanks Abhinav

[yuchaojiang]

Hi Abhinav, I will need to look into this as this wrapper was not written by me -- I will get back to you likely on Tuesday, if not sooner. Thanks.

[yuchaojiang]

@Ajaingithub There is a bug in the vignette. I've fixed it and made the update. I will upload another tutorial on how to generate pbmc.chromvar.rds soon.

[yuchaojiang]

Yes vignettes on preprocessing is available here http://htmlpreview.github.io/?https://github.com/yuchaojiang/TRIPOD/blob/main/vignettes/preprocessing_pbmc.html including the generating of the chromVAR domain.

The empty list was due to an error by that specific user. Please let us know if you have further questions.

On Feb 6, 2023, at 7:05 PM, collerlab-github @.**@.>> wrote:

Hi, I am wondering if the issue above has been fixed or not. I ran all the steps according to the vignette and I got an empty motifxTF and no motifs in the peakxmotif. You mentioned above about a tutorial for generating the chromvar.rds. Is it now available? Any help would be greatly appreciated. Thanks a lot!

— Reply to this email directly, view it on GitHubhttps://github.com/yuchaojiang/TRIPOD/issues/2#issuecomment-1419969019, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ACNKFSJEIE2MS6C7BRYSGLDWWGGVRANCNFSM6AAAAAAQ3DMK3U. You are receiving this because you modified the open/close state.Message ID: @.***>