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Hi,
I am trying to reproduce the tutorial: Analyzing PBMC scATAC-seq (https://satijalab.org/signac/articles/pbmc_vignette.html) using the following code (the same of the tutorial)
library(Signac)
library(Seurat)
library(GenomeInfoDb)
library(EnsDb.Hsapiens.v75)
library(ggplot2)
library(patchwork)
set.seed(1234)
counts <- Read10X_h5(filename = "Desktop/SC_ATAseq/atac_v1_pbmc_10k_filtered_peak_bc_matrix.h5")
metadata <- read.csv(
file = "Desktop/SC_ATAseq/atac_v1_pbmc_10k_singlecell.csv",
header = TRUE,
row.names = 1
)
chrom_assay <- CreateChromatinAssay(
counts = counts,
sep = c(":", "-"),
genome = 'hg19',
fragments = 'Desktop/SC_ATAseq/atac_v1_pbmc_10k_fragments.tsv.gz',
min.cells = 10,
min.features = 200
)
pbmc <- CreateSeuratObject(
counts = chrom_assay,
assay = "peaks",
meta.data = metadata
)
pbmc
##An object of class Seurat
##87561 features across 8728 samples within 1 assay
##Active assay: peaks (87561 features, 0 variable features)
pbmc[['peaks']]
##ChromatinAssay data with 87561 features for 8728 cells
##Variable features: 0
##Genome: hg19
##Annotation present: FALSE
##Motifs present: FALSE
##Fragment files: 1
granges(pbmc)
##GRanges object with 87561 ranges and 0 metadata columns:
## seqnames ranges strand
## <Rle> <IRanges> <Rle>
## [1] chr1 565107-565550 *
## [2] chr1 569174-569639 *
## [3] chr1 713460-714823 *
## [4] chr1 752422-753038 *
## [5] chr1 762106-763359 *
## ... ... ... ...
## [87557] chrY 58993392-58993760 *
## [87558] chrY 58994571-58994823 *
## [87559] chrY 58996352-58997331 *
## [87560] chrY 59001782-59002175 *
## [87561] chrY 59017143-59017246 *
## -------
## seqinfo: 24 sequences from an unspecified genome; no seqlengths
# extract gene annotations from EnsDb
annotations <- GetGRangesFromEnsDb(ensdb = EnsDb.Hsapiens.v75)
but I obtain this error
annotations <- GetGRangesFromEnsDb(ensdb = EnsDb.Hsapiens.v75)
Fetching data...OK
Parsing exons...OK
Defining introns...OK
Defining UTRs...Error in h(simpleError(msg, call)) :
error in evaluating the argument 'x' in selecting a method for function 'splitAsList': error in evaluating the argument 'x' in selecting a method for function 'end': error in evaluating the argument 'args' in selecting a method for function 'do.call': argument of length 0
also if I run
library(GenomeInfoDb)
whole.genome <- as(object = seqinfo(x = EnsDb.Hsapiens.v75), Class = "GRanges")
whole.genome <- keepStandardChromosomes(whole.genome, pruning.mode = "coarse")
annot <- biovizBase::crunch(obj = EnsDb.Hsapiens.v75, which = whole.genome[1],
columns = c("tx_id", "gene_name", "gene_id",
"gene_biotype"))
I obtain the same error.
annotations <- GetGRangesFromEnsDb(ensdb = EnsDb.Hsapiens.v75)
Fetching data...OK
Parsing exons...OK
Defining introns...OK
Defining UTRs...Error in h(simpleError(msg, call)) :
error in evaluating the argument 'x' in selecting a method for function 'splitAsList': error in evaluating the argument 'x' in selecting a method for function 'end': error in evaluating the argument 'args' in selecting a method for function 'do.call': argument of length 0
This is not an issue due to Signac package but this is an issue due to Bioconductor dependencies (I have already opened an issue on Signac (https://github.com/timoast/signac/issues/938)).
This is my Session info:
R version 4.0.3 (2020-10-10)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Big Sur 10.16
Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib
locale:
[1] it_IT.UTF-8/it_IT.UTF-8/it_IT.UTF-8/C/it_IT.UTF-8/it_IT.UTF-8
attached base packages:
[1] stats4 stats graphics grDevices utils datasets methods base
other attached packages:
[1] patchwork_1.1.1 ggplot2_3.3.5 EnsDb.Hsapiens.v75_2.99.0
[4] ensembldb_2.14.1 AnnotationFilter_1.14.0 GenomicFeatures_1.42.3
[7] AnnotationDbi_1.52.0 Biobase_2.50.0 GenomicRanges_1.42.0
[10] GenomeInfoDb_1.31.1 IRanges_2.24.1 S4Vectors_0.28.1
[13] BiocGenerics_0.40.0 SeuratObject_4.0.4 Seurat_4.0.4
[16] Signac_1.5.0.9000
loaded via a namespace (and not attached):
[1] utf8_1.2.2 reticulate_1.23 tidyselect_1.1.1
[4] RSQLite_2.2.9 htmlwidgets_1.5.4 grid_4.0.3
[7] docopt_0.7.1 BiocParallel_1.24.1 Rtsne_0.15
[10] devtools_2.4.3 munsell_0.5.0 codetools_0.2-18
[13] ica_1.0-2 future_1.23.0 miniUI_0.1.1.1
[16] withr_2.4.3 colorspace_2.0-2 knitr_1.37
[19] rstudioapi_0.13 ROCR_1.0-11 tensor_1.5
[22] listenv_0.8.0 MatrixGenerics_1.2.1 slam_0.1-49
[25] GenomeInfoDbData_1.2.4 polyclip_1.10-0 bit64_4.0.5
[28] farver_2.1.0 rprojroot_2.0.2 parallelly_1.30.0
[31] vctrs_0.3.8.9001 generics_0.1.1 xfun_0.29
[34] biovizBase_1.38.0 BiocFileCache_1.14.0 lsa_0.73.2
[37] ggseqlogo_0.1 R6_2.5.1 hdf5r_1.3.5
[40] DelayedArray_0.16.3 bitops_1.0-7 spatstat.utils_2.3-0
[43] cachem_1.0.6 assertthat_0.2.1 promises_1.2.0.1
[46] scales_1.1.1 nnet_7.3-17 gtable_0.3.0
[49] globals_0.14.0 processx_3.5.2 goftest_1.2-3
[52] rlang_0.99.0.9003 RcppRoll_0.3.0 splines_4.0.3
[55] rtracklayer_1.50.0 lazyeval_0.2.2 dichromat_2.0-0
[58] checkmate_2.0.0 spatstat.geom_2.3-1 reshape2_1.4.4
[61] abind_1.4-5 backports_1.4.1 httpuv_1.6.5
[64] Hmisc_4.6-0 tools_4.0.3 usethis_2.1.5
[67] ellipsis_0.3.2 spatstat.core_2.3-2 RColorBrewer_1.1-2
[70] sessioninfo_1.2.2 ggridges_0.5.3 Rcpp_1.0.7
[73] plyr_1.8.6 base64enc_0.1-3 progress_1.2.2
[76] zlibbioc_1.36.0 purrr_0.3.4 RCurl_1.98-1.5
[79] ps_1.6.0 prettyunits_1.1.1 rpart_4.1-15
[82] openssl_1.4.6 deldir_1.0-6 pbapply_1.5-0
[85] cowplot_1.1.1 zoo_1.8-9 SummarizedExperiment_1.20.0
[88] ggrepel_0.9.1 cluster_2.1.2 fs_1.5.2
[91] tinytex_0.36 magrittr_2.0.1 data.table_1.14.2
[94] scattermore_0.7 lmtest_0.9-39 RANN_2.6.1
[97] SnowballC_0.7.0 ProtGenerics_1.22.0 fitdistrplus_1.1-6
[100] matrixStats_0.61.0 pkgload_1.2.4 hms_1.1.1
[103] mime_0.12 xtable_1.8-4 XML_3.99-0.8
[106] jpeg_0.1-9 sparsesvd_0.2 gridExtra_2.3
[109] testthat_3.1.1 compiler_4.0.3 biomaRt_2.46.3
[112] tibble_3.1.6 KernSmooth_2.23-20 crayon_1.4.2
[115] htmltools_0.5.2 mgcv_1.8-38 later_1.3.0
[118] Formula_1.2-4 tidyr_1.1.4 DBI_1.1.2
[121] tweenr_1.0.2 dbplyr_2.1.1 rappdirs_0.3.3
[124] MASS_7.3-55 Matrix_1.4-0 cli_3.1.0
[127] parallel_4.0.3 igraph_1.2.10 pkgconfig_2.0.3
[130] GenomicAlignments_1.26.0 foreign_0.8-82 plotly_4.10.0
[133] spatstat.sparse_2.1-0 xml2_1.3.3 XVector_0.30.0
[136] VariantAnnotation_1.36.0 stringr_1.4.0 callr_3.7.0
[139] digest_0.6.29 sctransform_0.3.2 RcppAnnoy_0.0.19
[142] spatstat.data_2.1-2 Biostrings_2.58.0 leiden_0.3.9
[145] fastmatch_1.1-3 htmlTable_2.4.0 uwot_0.1.11
[148] curl_4.3.2 shiny_1.7.1 Rsamtools_2.6.0
[151] lifecycle_1.0.1 nlme_3.1-153 jsonlite_1.7.3
[154] BSgenome_1.58.0 desc_1.4.0 viridisLite_0.4.0
[157] askpass_1.1 fansi_1.0.2 pillar_1.6.4
[160] lattice_0.20-45 fastmap_1.1.0 httr_1.4.2
[163] pkgbuild_1.3.1 survival_3.2-13 glue_1.6.0
[166] remotes_2.4.2 qlcMatrix_0.9.7 png_0.1-7
[169] bit_4.0.4 ggforce_0.3.3 stringi_1.7.6
[172] blob_1.2.2 latticeExtra_0.6-29 memoise_2.0.1
[175] dplyr_1.0.7 irlba_2.3.5 future.apply_1.8.1
I have tried to see if someone else had this issue, I have tried to install different version of Seurat and Signac but I did not find how to figure out.
Any help would be greatly appreciated. Best wishes Francesco
Dear James,
thank you very much, I upgraded to R-4.1.2 and Bioc-3.14 and I solved the issue.
Best wishes Francesco