TSSEnrichment argument "slot" is missing, with no default

[lianov]

Hello!

With Seurat V 5.0.2 , TSSEnrichment fails with in an attempt to look for slot instead of layer:

Error in slot(object = object, name = layer) : 
  argument "slot" is missing, with no default

Using vignette code from: https://stuartlab.org/signac/articles/pbmc_vignette, I am able to reproduce the same issue I am finding in my own analysis. For the vignette code, the following should be sufficient to reproduce it:

library(Signac)
library(Seurat)
library(EnsDb.Hsapiens.v75)
library(ggplot2)
library(patchwork)

counts <- Read10X_h5(filename = "./atac_v1_pbmc_10k_filtered_peak_bc_matrix.h5")
metadata <- read.csv(
  file = "./atac_v1_pbmc_10k_singlecell.csv",
  header = TRUE,
  row.names = 1
)

chrom_assay <- CreateChromatinAssay(
  counts = counts,
  sep = c(":", "-"),
  fragments = './atac_v1_pbmc_10k_fragments.tsv.gz',
  min.cells = 10,
  min.features = 200
)

pbmc <- CreateSeuratObject(
  counts = chrom_assay,
  assay = "peaks",
  meta.data = metadata
)

pbmc[['peaks']]

granges(pbmc)

# extract gene annotations from EnsDb
annotations <- GetGRangesFromEnsDb(ensdb = EnsDb.Hsapiens.v75)

# change to UCSC style since the data was mapped to hg19
seqlevels(annotations) <- paste0('chr', seqlevels(annotations))
genome(annotations) <- "hg19"

# add the gene information to the object
Annotation(pbmc) <- annotations

# compute nucleosome signal score per cell
pbmc <- NucleosomeSignal(object = pbmc)

# compute TSS enrichment score per cell
pbmc <- TSSEnrichment(object = pbmc, fast = FALSE) #error: argument "slot" is missing, with no default

Below is my local computer environment, but I am also seeing the issue from a custom made Singularity container (not shown here, can updated if needed; both environments contain Seurat V5 (5.0.2) + latest version of Signac, 1.12.0).

R version 4.3.1 (2023-06-16)
Platform: x86_64-apple-darwin20 (64-bit)
Running under: macOS Monterey 12.7.1

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib 
LAPACK: /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libRlapack.dylib;  LAPACK version 3.11.0

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

time zone: America/Chicago
tzcode source: internal

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

other attached packages:
 [1] patchwork_1.2.0           ggplot2_3.5.0             EnsDb.Hsapiens.v75_2.99.0 ensembldb_2.24.1          AnnotationFilter_1.24.0   GenomicFeatures_1.52.2    AnnotationDbi_1.62.2      Biobase_2.60.0           
 [9] GenomicRanges_1.52.1      GenomeInfoDb_1.36.4       IRanges_2.34.1            S4Vectors_0.38.2          BiocGenerics_0.46.0       Seurat_5.0.2              SeuratObject_5.0.1        sp_2.1-3                 
[17] Signac_1.12.0            

loaded via a namespace (and not attached):
  [1] RcppAnnoy_0.0.22            splines_4.3.1               later_1.3.2                 BiocIO_1.10.0               bitops_1.0-7                filelock_1.0.3              tibble_3.2.1               
  [8] polyclip_1.10-6             rpart_4.1.23                XML_3.99-0.16.1             fastDummies_1.7.3           lifecycle_1.0.4             hdf5r_1.3.9                 globals_0.16.2             
 [15] lattice_0.22-5              MASS_7.3-60.0.1             backports_1.4.1             magrittr_2.0.3              rmarkdown_2.25              Hmisc_5.1-1                 plotly_4.10.4              
 [22] yaml_2.3.8                  httpuv_1.6.14               sctransform_0.4.1           spam_2.10-0                 spatstat.sparse_3.0-3       reticulate_1.35.0           cowplot_1.1.3              
 [29] pbapply_1.7-2               DBI_1.2.2                   RColorBrewer_1.1-3          abind_1.4-5                 zlibbioc_1.46.0             Rtsne_0.17                  purrr_1.0.2                
 [36] biovizBase_1.48.0           RCurl_1.98-1.14             nnet_7.3-19                 VariantAnnotation_1.46.0    rappdirs_0.3.3              GenomeInfoDbData_1.2.10     ggrepel_0.9.5              
 [43] irlba_2.3.5.1               listenv_0.9.1               spatstat.utils_3.0-4        goftest_1.2-3               RSpectra_0.16-1             spatstat.random_3.2-3       fitdistrplus_1.1-11        
 [50] parallelly_1.37.1           DelayedArray_0.26.7         leiden_0.4.3.1              codetools_0.2-19            RcppRoll_0.3.0              xml2_1.3.6                  tidyselect_1.2.0           
 [57] base64enc_0.1-3             matrixStats_1.2.0           BiocFileCache_2.8.0         spatstat.explore_3.2-6      GenomicAlignments_1.36.0    jsonlite_1.8.8              Formula_1.2-5              
 [64] ellipsis_0.3.2              progressr_0.14.0            ggridges_0.5.6              survival_3.5-8              tools_4.3.1                 progress_1.2.3              ica_1.0-3                  
 [71] Rcpp_1.0.12                 glue_1.7.0                  gridExtra_2.3               xfun_0.42                   MatrixGenerics_1.12.3       dplyr_1.1.4                 withr_3.0.0                
 [78] BiocManager_1.30.22         fastmap_1.1.1               fansi_1.0.6                 digest_0.6.34               R6_2.5.1                    mime_0.12                   colorspace_2.1-0           
 [85] scattermore_1.2             tensor_1.5                  dichromat_2.0-0.1           spatstat.data_3.0-4         biomaRt_2.56.1              RSQLite_2.3.5               utf8_1.2.4                 
 [92] tidyr_1.3.1                 generics_0.1.3              data.table_1.15.2           rtracklayer_1.60.1          S4Arrays_1.0.6              prettyunits_1.2.0           httr_1.4.7                 
 [99] htmlwidgets_1.6.4           uwot_0.1.16                 pkgconfig_2.0.3             gtable_0.3.4                blob_1.2.4                  lmtest_0.9-40               XVector_0.40.0             
[106] htmltools_0.5.7             dotCall64_1.1-1             ProtGenerics_1.32.0         scales_1.3.0                png_0.1-8                   knitr_1.45                  rstudioapi_0.15.0          
[113] reshape2_1.4.4              rjson_0.2.21                checkmate_2.3.1             nlme_3.1-164                curl_5.2.1                  zoo_1.8-12                  cachem_1.0.8               
[120] stringr_1.5.1               KernSmooth_2.23-22          parallel_4.3.1              miniUI_0.1.1.1              foreign_0.8-86              restfulr_0.0.15             pillar_1.9.0               
[127] grid_4.3.1                  vctrs_0.6.5                 RANN_2.6.1                  promises_1.2.1              dbplyr_2.4.0                xtable_1.8-4                cluster_2.1.6              
[134] htmlTable_2.4.2             evaluate_0.23               cli_3.6.2                   compiler_4.3.1              Rsamtools_2.16.0            rlang_1.1.3                 crayon_1.5.2               
[141] future.apply_1.11.1         plyr_1.8.9                  stringi_1.8.3               viridisLite_0.4.2           deldir_2.0-4                BiocParallel_1.34.2         munsell_0.5.0              
[148] Biostrings_2.68.1           lazyeval_0.2.2              spatstat.geom_3.2-9         Matrix_1.6-5                BSgenome_1.68.0             RcppHNSW_0.6.0              hms_1.1.3                  
[155] bit64_4.0.5                 future_1.33.1               KEGGREST_1.40.1             shiny_1.8.0                 SummarizedExperiment_1.30.2 ROCR_1.0-11                 igraph_2.0.2               
[162] memoise_2.0.1               fastmatch_1.1-4             bit_4.0.5                  
> 

[timoast]

Please see #1538