'Error in density.default(x = query.feature[[featmatch]], kernel = "gaussian", : 'x' contains missing values' while running JASPAR2020 for motif enrichment analyses: #5
Description
While everything else ran smoothly, there is an issue while running JASPAR.
Also in the script earlier (shown here below):
> library(TFBSTools)
> library(JASPAR2020)
>
> pfm <- getMatrixSet(
+ x = JASPAR2020,
+ opts = list(collection = "CORE", tax_group = 'vertebrates', all_versions = FALSE)
+ )
> df_pfm <- data.frame(t(sapply(pfm, function(x)
+ c(id=x@ID, name=x@name, symbol=ifelse(!is.null(x@tags$symbol),x@tags$symbol,NA)))))
>
> seurat <- AddMotifs(seurat, genome = BSgenome.Hsapiens.UCSC.hg38, pfm = pfm)
Building motif matrix
Warning in CreateMotifMatrix(features = object, pwm = pfm, genome = genome, :
Not all seqlevels present in supplied genome
Finding motif positions
Creating Motif object
Warning in RegionStats.default(object = regions, genome = genome, verbose = verbose, :
Not all seqlevels present in supplied genome
Warning messages:
1: 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]
2: 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]
> open_peaks <- AccessiblePeaks(seurat)
> peaks_matched <- MatchRegionStats(meta.feature = seurat[['ATAC']]@meta.features[open_peaks, ],
+ query.feature = seurat[['ATAC']]@meta.features[top_peaks_ct$feature, ],
+ n = 50000)
Matching GC.percent distribution
Error in density.default(x = query.feature[[featmatch]], kernel = "gaussian", :
'x' contains missing values
> sessionInfo()
R version 4.2.1 (2022-06-23)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.5 LTS
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/liblapack.so.3
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8
[4] LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats4 stats graphics grDevices utils datasets methods base
other attached packages:
[1] BSgenome.Hsapiens.UCSC.hg38_1.4.5 BSgenome_1.66.3
[3] rtracklayer_1.58.0 Biostrings_2.66.0
[5] XVector_0.38.0 GenomicRanges_1.50.2
[7] GenomeInfoDb_1.34.9 IRanges_2.32.0
[9] S4Vectors_0.36.2 BiocGenerics_0.44.0
[11] JASPAR2020_0.99.10 TFBSTools_1.36.0
[13] presto_1.0.0 data.table_1.15.2
[15] Rcpp_1.0.12 simspec_0.0.0.9000
[17] Matrix_1.6-5 dplyr_1.1.4
[19] Signac_1.12.0 Seurat_5.0.2
[21] SeuratObject_5.0.1 sp_2.1-3
loaded via a namespace (and not attached):
[1] utf8_1.2.4 R.utils_2.12.3 spatstat.explore_3.2-6
[4] reticulate_1.35.0 tidyselect_1.2.0 AnnotationDbi_1.60.2
[7] poweRlaw_0.80.0 RSQLite_2.3.5 htmlwidgets_1.6.4
[10] grid_4.2.1 BiocParallel_1.32.6 Rtsne_0.17
[13] munsell_0.5.0 codetools_0.2-18 ica_1.0-3
[16] future_1.33.1 miniUI_0.1.1.1 withr_3.0.0
[19] spatstat.random_3.2-3 colorspace_2.1-0 progressr_0.14.0
[22] Biobase_2.58.0 rstudioapi_0.15.0 ROCR_1.0-11
[25] tensor_1.5 listenv_0.9.1 MatrixGenerics_1.10.0
[28] labeling_0.4.3 GenomeInfoDbData_1.2.9 polyclip_1.10-6
[31] bit64_4.0.5 farver_2.1.1 parallelly_1.37.1
[34] vctrs_0.6.5 generics_0.1.3 R6_2.5.1
[37] bitops_1.0-7 spatstat.utils_3.0-4 cachem_1.0.8
[40] DelayedArray_0.24.0 promises_1.2.1 BiocIO_1.8.0
[43] scales_1.3.0 gtable_0.3.4 globals_0.16.2
[46] goftest_1.2-3 spam_2.10-0 seqLogo_1.64.0
[49] rlang_1.1.3 RcppRoll_0.3.0 splines_4.2.1
[52] lazyeval_0.2.2 spatstat.geom_3.2-9 BiocManager_1.30.22
[55] yaml_2.3.8 reshape2_1.4.4 abind_1.4-5
[58] httpuv_1.6.14 tools_4.2.1 ggplot2_3.5.0
[61] ellipsis_0.3.2 RColorBrewer_1.1-3 ggridges_0.5.6
[64] plyr_1.8.9 zlibbioc_1.44.0 purrr_1.0.2
[67] RCurl_1.98-1.14 deldir_2.0-4 pbapply_1.7-2
[70] cowplot_1.1.3 zoo_1.8-12 SummarizedExperiment_1.28.0
[73] ggrepel_0.9.5 cluster_2.1.3 motifmatchr_1.20.0
[76] magrittr_2.0.3 RSpectra_0.16-1 scattermore_1.2
[79] lmtest_0.9-40 RANN_2.6.1 fitdistrplus_1.1-11
[82] matrixStats_1.2.0 hms_1.1.3 patchwork_1.2.0
[85] mime_0.12 xtable_1.8-4 XML_3.99-0.16.1
[88] fastDummies_1.7.3 gridExtra_2.3 compiler_4.2.1
[91] tibble_3.2.1 KernSmooth_2.23-20 crayon_1.5.2
[94] R.oo_1.26.0 htmltools_0.5.7 later_1.3.2
[97] tzdb_0.4.0 tidyr_1.3.1 DBI_1.2.2
[100] MASS_7.3-57 readr_2.1.5 cli_3.6.2
[103] R.methodsS3_1.8.2 parallel_4.2.1 dotCall64_1.1-1
[106] igraph_2.0.2 pkgconfig_2.0.3 GenomicAlignments_1.34.1
[109] TFMPvalue_0.0.9 plotly_4.10.4 spatstat.sparse_3.0-3
[112] annotate_1.76.0 DirichletMultinomial_1.40.0 stringr_1.5.1
[115] digest_0.6.34 sctransform_0.4.1 RcppAnnoy_0.0.22
[118] pracma_2.4.4 CNEr_1.34.0 spatstat.data_3.0-4
[121] leiden_0.4.3.1 fastmatch_1.1-4 uwot_0.1.16
[124] restfulr_0.0.15 shiny_1.8.0 Rsamtools_2.14.0
[127] gtools_3.9.5 rjson_0.2.21 lifecycle_1.0.4
[130] nlme_3.1-157 jsonlite_1.8.8 viridisLite_0.4.2
[133] fansi_1.0.6 pillar_1.9.0 lattice_0.20-45
[136] GO.db_3.16.0 KEGGREST_1.38.0 fastmap_1.1.1
[139] httr_1.4.7 survival_3.3-1 glue_1.7.0
[142] png_0.1-8 bit_4.0.5 stringi_1.8.3
[145] blob_1.2.4 RcppHNSW_0.6.0 caTools_1.18.2
[148] memoise_2.0.1 irlba_2.3.5.1 future.apply_1.11.1