Hi,
LinkPeaks produces an unexpected error when I try to run it:
DefaultAssay(rv2.ss) <- "peaks"
linkpeaks.out <- LinkPeaks(rv2.ss,
peak.assay = "peaks",
expression.assay = "RNA",
n_sample = 200,
genes.use = lp.genes,
min.distance = 2000,
distance = 50000)
Error:
Testing 4 genes and 107523 peaks
Error in LinkPeaks(rv2.ss, peak.assay = "peaks", expression.assay = "RNA", :
No peaks fall within distance threshold
Have you set the proper genome and seqlevelsStyle for peaks assay?
Here lp.genes is a vector containing ENSMUS IDs (as are the rownames of RNA assay) for which I know there are expected to be correlated peaks within the distance parameter. Thus, the error shouldn't rise from that. The data object contains data from typical chromosomes, but seqlevels returns also other chr-tags:
> seqlevels(rv2.ss) [1] "chr1" "chr2" "chr3" "chr4" "chr5" "chr6" "chr7" "chr8" [9] "chr9" "chr10" "chr11" "chr12" "chr13" "chr14" "chr15" "chr16" [17] "chr17" "chr18" "chr19" "chrX" "chrY" "chrM" "chr1_GL456210_random" "chr1_GL456211_random" [25] "chr1_GL456212_random" "chr1_GL456213_random" "chr1_GL456221_random" "chr4_GL456216_random" "chr4_GL456350_random" "chr4_JH584292_random" "chr4_JH584293_random" "chr4_JH584294_random" [33] "chr4_JH584295_random" "chr5_GL456354_random" "chr5_JH584296_random" "chr5_JH584297_random" "chr5_JH584298_random" "chr5_JH584299_random" "chr7_GL456219_random" "chrX_GL456233_random" [41] "chrY_JH584300_random" "chrY_JH584301_random" "chrY_JH584302_random" "chrY_JH584303_random" "chrUn_GL456239" "chrUn_GL456359" "chrUn_GL456360" "chrUn_GL456366" [49] "chrUn_GL456367" "chrUn_GL456368" "chrUn_GL456370" "chrUn_GL456372" "chrUn_GL456378" "chrUn_GL456379" "chrUn_GL456381" "chrUn_GL456382" [57] "chrUn_GL456383" "chrUn_GL456385" "chrUn_GL456387" "chrUn_GL456389" "chrUn_GL456390" "chrUn_GL456392" "chrUn_GL456393" "chrUn_GL456394" [65] "chrUn_GL456396" "chrUn_JH584304"
I'm using R version 4.1.1 and Signac version 1.4.0. Info on these and other properties can be found from session info below
> sessionInfo() R version 4.1.1 (2021-08-10) Platform: x86_64-pc-linux-gnu (64-bit) Running under: CentOS Linux 7 (Core) Matrix products: default BLAS/LAPACK: /opt/intel/oneapi/mkl/2021.2.0/lib/intel64/libmkl_gf_lp64.so.1 locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 LC_PAPER=en_US.UTF-8 [8] LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] SeuratObject_4.0.2 Seurat_4.0.5 forcats_0.5.1 stringr_1.4.0 dplyr_1.0.7 purrr_0.3.4 readr_2.0.2 tidyr_1.1.4 tibble_3.1.5 ggplot2_3.3.3 [11] tidyverse_1.3.1 Signac_1.4.0 loaded via a namespace (and not attached): [1] readxl_1.3.1 backports_1.2.1 fastmatch_1.1-3 plyr_1.8.6 igraph_1.2.6 lazyeval_0.2.2 splines_4.1.1 BiocParallel_1.26.2 [9] listenv_0.8.0 scattermore_0.7 SnowballC_0.7.0 GenomeInfoDb_1.26.7 digest_0.6.28 htmltools_0.5.2 fansi_0.5.0 magrittr_2.0.1 [17] tensor_1.5 cluster_2.1.2 ROCR_1.0-11 tzdb_0.2.0 globals_0.14.0 Biostrings_2.60.2 modelr_0.1.8 matrixStats_0.61.0 [25] docopt_0.7.1 spatstat.sparse_2.0-0 colorspace_2.0-2 rvest_1.0.1 ggrepel_0.9.1 haven_2.4.3 sparsesvd_0.2 crayon_1.4.1 [33] RCurl_1.98-1.5 jsonlite_1.7.2 spatstat.data_2.1-0 survival_3.2-11 zoo_1.8-9 glue_1.4.2 polyclip_1.10-0 gtable_0.3.0 [41] zlibbioc_1.38.0 XVector_0.32.0 leiden_0.3.9 future.apply_1.8.1 BiocGenerics_0.36.1 abind_1.4-5 scales_1.1.1 DBI_1.1.1 [49] miniUI_0.1.1.1 Rcpp_1.0.7 viridisLite_0.4.0 xtable_1.8-4 reticulate_1.22 spatstat.core_2.3-0 stats4_4.1.1 htmlwidgets_1.5.4 [57] httr_1.4.2 RColorBrewer_1.1-2 ellipsis_0.3.2 ica_1.0-2 pkgconfig_2.0.3 farver_2.1.0 ggseqlogo_0.1 uwot_0.1.10 [65] dbplyr_2.1.1 deldir_0.2-10 utf8_1.2.2 labeling_0.4.2 tidyselect_1.1.1 rlang_0.4.12 reshape2_1.4.4 later_1.3.0 [73] cellranger_1.1.0 munsell_0.5.0 tools_4.1.1 cli_3.1.0 generics_0.1.0 broom_0.7.6 ggridges_0.5.3 fastmap_1.1.0 [81] goftest_1.2-2 fs_1.5.0 fitdistrplus_1.1-6 RANN_2.6.1 pbapply_1.5-0 future_1.21.0 nlme_3.1-152 mime_0.12 [89] slam_0.1-48 RcppRoll_0.3.0 xml2_1.3.2 compiler_4.1.1 rstudioapi_0.13 plotly_4.9.4.1 png_0.1-7 spatstat.utils_2.2-0 [97] reprex_2.0.1 tweenr_1.0.2 stringi_1.7.5 lattice_0.20-44 Matrix_1.3-4 vctrs_0.3.8 pillar_1.6.3 lifecycle_1.0.1 [105] spatstat.geom_2.2-2 lmtest_0.9-38 RcppAnnoy_0.0.19 data.table_1.14.0 cowplot_1.1.1 bitops_1.0-7 irlba_2.3.3 httpuv_1.6.3 [113] patchwork_1.1.1 GenomicRanges_1.42.0 R6_2.5.1 promises_1.2.0.1 KernSmooth_2.23-20 gridExtra_2.3 lsa_0.73.2 IRanges_2.26.0 [121] parallelly_1.28.1 codetools_0.2-18 MASS_7.3-54 assertthat_0.2.1 withr_2.4.2 qlcMatrix_0.9.7 sctransform_0.3.2 Rsamtools_2.8.0 [129] S4Vectors_0.30.2 GenomeInfoDbData_1.2.6 mgcv_1.8-36 parallel_4.1.1 hms_1.1.1 grid_4.1.1 rpart_4.1-15 Rtsne_0.15 [137] ggforce_0.3.3 lubridate_1.7.10 shiny_1.7.1
Thank you!
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