Hello!
I am encountering an issue with the FindMotifs function which returns the error below:
enriched.motifs <- FindMotifs(object = so_filt,features = te_peaks, assay = 'peaks', background = 20000)
Error in MatchRegionStats(meta.feature = mf.choose, query.feature = mf.query, : 1 not present in meta.features
Traceback:
- FindMotifs(object = so_filt, features = te_peaks, assay = "peaks",
. background = 20000)- MatchRegionStats(meta.feature = mf.choose, query.feature = mf.query,
. regions = features, n = background, verbose = verbose, ...)- stop(i, " not present in meta.features")
The same error arises with the atac_small data:
test_peaks <- rownames(atac_small@assays$peaks@meta.features[1:100,]) FindMotifs(atac_small, features = test_peaks, background = 200)
Selecting background regions to match input sequence characteristics
Error in MatchRegionStats(meta.feature = mf.choose, query.feature = mf.query, : 1 not present in meta.features
Traceback:
- FindMotifs(atac_small, features = test_peaks, background = 200)
- MatchRegionStats(meta.feature = mf.choose, query.feature = mf.query,
. regions = features, n = background, verbose = verbose, ...)- stop(i, " not present in meta.features")
Any help would be kindly appreciated.
Cheers!
--Grigorios
Here's what my sessionInfo() looks like
R version 4.0.3 (2020-10-10)
Platform: x86_64-conda-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)Matrix products: default
BLAS/LAPACK: /vsc-hard-mounts/leuven-data/341/vsc34172/miniconda3/envs/r_env/lib/libopenblasp-r0.3.12.solocale:
[1] Cattached base packages:
[1] stats4 parallel stats graphics grDevices utils datasets
[8] methods baseother attached packages:
[1] eulerr_6.1.0 future.apply_1.7.0
[3] future_1.21.0 tidyr_1.1.3
[5] reticulate_1.18 leiden_0.3.7
[7] hdf5r_1.3.3 patchwork_1.1.1
[9] ggplot2_3.3.3 EnsDb.Hsapiens.v86_2.99.0
[11] ensembldb_2.14.0 AnnotationFilter_1.14.0
[13] GenomicFeatures_1.42.2 AnnotationDbi_1.52.0
[15] Biobase_2.50.0 GenomicRanges_1.42.0
[17] GenomeInfoDb_1.26.4 IRanges_2.24.1
[19] S4Vectors_0.28.1 BiocGenerics_0.36.0
[21] SeuratObject_4.0.0 Seurat_4.0.1
[23] Signac_1.1.1loaded via a namespace (and not attached):
[1] utf8_1.2.1 tidyselect_1.1.0
[3] RSQLite_2.2.5 htmlwidgets_1.5.3
[5] grid_4.0.3 BiocParallel_1.24.1
[7] Rtsne_0.15 munsell_0.5.0
[9] codetools_0.2-18 ica_1.0-2
[11] pbdZMQ_0.3-5 miniUI_0.1.1.1
[13] withr_2.4.1 colorspace_2.0-0
[15] OrganismDbi_1.32.0 knitr_1.31
[17] uuid_0.1-4 rstudioapi_0.13
[19] ROCR_1.0-11 tensor_1.5
[21] listenv_0.8.0 labeling_0.4.2
[23] MatrixGenerics_1.2.1 repr_1.1.3
[25] GenomeInfoDbData_1.2.4 polyclip_1.10-0
[27] farver_2.1.0 bit64_4.0.5
[29] parallelly_1.24.0 vctrs_0.3.7
[31] generics_0.1.0 xfun_0.22
[33] biovizBase_1.38.0 BiocFileCache_1.14.0
[35] lsa_0.73.2 ggseqlogo_0.1
[37] R6_2.5.0 reshape_0.8.8
[39] bitops_1.0-6 spatstat.utils_2.1-0
[41] cachem_1.0.4 DelayedArray_0.16.3
[43] assertthat_0.2.1 promises_1.2.0.1
[45] scales_1.1.1 nnet_7.3-15
[47] gtable_0.3.0 globals_0.14.0
[49] goftest_1.2-2 ggbio_1.38.0
[51] rlang_0.4.10 RcppRoll_0.3.0
[53] splines_4.0.3 rtracklayer_1.50.0
[55] lazyeval_0.2.2 dichromat_2.0-0
[57] spatstat.geom_2.0-1 checkmate_2.0.0
[59] BiocManager_1.30.12 reshape2_1.4.4
[61] abind_1.4-5 backports_1.2.1
[63] httpuv_1.5.5 SeuratDisk_0.0.0.9019
[65] Hmisc_4.5-0 RBGL_1.66.0
[67] tools_4.0.3 ellipsis_0.3.1
[69] spatstat.core_2.0-0 RColorBrewer_1.1-2
[71] ggridges_0.5.3 Rcpp_1.0.6
[73] plyr_1.8.6 base64enc_0.1-3
[75] progress_1.2.2 zlibbioc_1.36.0
[77] purrr_0.3.4 RCurl_1.98-1.3
[79] prettyunits_1.1.1 rpart_4.1-15
[81] openssl_1.4.3 deldir_0.2-10
[83] pbapply_1.4-3 cowplot_1.1.1
[85] zoo_1.8-9 SummarizedExperiment_1.20.0
[87] ggrepel_0.9.1 cluster_2.1.1
[89] magrittr_2.0.1 RSpectra_0.16-0
[91] data.table_1.14.0 scattermore_0.7
[93] lmtest_0.9-38 RANN_2.6.1
[95] SnowballC_0.7.0 ProtGenerics_1.22.0
[97] fitdistrplus_1.1-3 matrixStats_0.58.0
[99] hms_1.0.0 mime_0.10
[101] evaluate_0.14 xtable_1.8-4
[103] XML_3.99-0.6 jpeg_0.1-8.1
[105] gridExtra_2.3 compiler_4.0.3
[107] biomaRt_2.46.3 tibble_3.1.0
[109] KernSmooth_2.23-18 crayon_1.4.1
[111] htmltools_0.5.1.1 mgcv_1.8-34
[113] later_1.1.0.1 Formula_1.2-4
[115] DBI_1.1.1 tweenr_1.0.2
[117] dbplyr_2.1.0 MASS_7.3-53.1
[119] rappdirs_0.3.3 Matrix_1.3-2
[121] cli_2.3.1 igraph_1.2.6
[123] pkgconfig_2.0.3 GenomicAlignments_1.26.0
[125] foreign_0.8-81 IRdisplay_1.0
[127] plotly_4.9.3 spatstat.sparse_2.0-0
[129] xml2_1.3.2 XVector_0.30.0
[131] stringr_1.4.0 VariantAnnotation_1.36.0
[133] digest_0.6.27 sctransform_0.3.2
[135] RcppAnnoy_0.0.18 graph_1.68.0
[137] spatstat.data_2.1-0 Biostrings_2.58.0
[139] polylabelr_0.2.0 fastmatch_1.1-0
[141] htmlTable_2.1.0 uwot_0.1.10
[143] curl_4.3 shiny_1.6.0
[145] Rsamtools_2.6.0 lifecycle_1.0.0
[147] nlme_3.1-152 jsonlite_1.7.2
[149] viridisLite_0.3.0 askpass_1.1
[151] BSgenome_1.58.0 fansi_0.4.2
[153] pillar_1.5.1 GGally_2.1.1
[155] lattice_0.20-41 fastmap_1.1.0
[157] httr_1.4.2 survival_3.2-10
[159] glue_1.4.2 png_0.1-7
[161] bit_4.0.4 ggforce_0.3.3
[163] stringi_1.5.3 blob_1.2.1
[165] latticeExtra_0.6-29 memoise_2.0.0
[167] IRkernel_1.1.1 dplyr_1.0.5
[169] irlba_2.3.3
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