Error when projecting reference dataset with on-disc data matrix: "Error in h(simpleError(msg, call)) : error in evaluating the argument 'x' in selecting a method for function 't': Argument 'x' must be of type logical, integer or numeric, not 'list'"

[sbamopoulos]

Hello,

after lengthy debugging I noticed that there is an issue when projecting a reference dataset onto a query dataset if the reference dataset "data" matrix is not stored in memory, but instead is stored on disk using the BPcells package. Here is a sample code:

library(Seurat)
library(SeuratObject)
library(BPCells)

query.obj <- readRDS("path1.rds")
ref.obj <- readRDS("path2.rds")

tanc <- FindTransferAnchors(reference = ref.obj, reference.assay = "RNA", reference.reduction = "rpca_integrated",
                            query = query.obj, query.assay = "RNA", scale = T, project.query = F,
                            normalization.method = "LogNormalize", dims = 1:30, verbose = T)

query.obj <- MapQuery(anchorset = tanc, query = query.obj, reference = ref.obj, refdata = "annotation_ref", 
                   reference.reduction = "rpca_integrated", new.reduction.name = "pcaref")

This produces this non-informative error:

Projecting cell embeddings
Error in h(simpleError(msg, call)) : 
  error in evaluating the argument 'x' in selecting a method for function 't': Argument 'x' must be of type logical, integer or numeric, not 'list'

However, if I convert the "data" matrix to an in memory matrix, as per your tutorial:

ref.obj[["RNA"]]$data <- as(object = ref.obj[["RNA"]]$data, Class = "dgCMatrix")

The code runs through without an error:

Projecting cell embeddings
Finding neighborhoods
Finding anchors
	Found 2346 anchors
Finding neighborhoods
Finding anchors
	Found 1874 anchors
Finding neighborhoods
Finding anchors
	Found 2081 anchors
Finding neighborhoods
Finding anchors
	Found 2674 anchors
Finding neighborhoods
Finding anchors
	Found 1497 anchors
Finding neighborhoods
Finding anchors
	Found 1582 anchors
Finding neighborhoods
Finding anchors
	Found 1815 anchors
Finding neighborhoods
Finding anchors
	Found 1043 anchors
Finding neighborhoods
Finding anchors
	Found 2100 anchors
Finding neighborhoods
Finding anchors
	Found 1221 anchors
Finding neighborhoods
Finding anchors
	Found 2547 anchors

sessionInfo()
R version 4.3.3 (2024-02-29 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 11 x64 (build 22631)

Matrix products: default


locale:
[1] LC_COLLATE=English_Germany.utf8  LC_CTYPE=English_Germany.utf8    LC_MONETARY=English_Germany.utf8 LC_NUMERIC=C                    
[5] LC_TIME=English_Germany.utf8    

time zone: Europe/Berlin
tzcode source: internal

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

other attached packages:
 [1] dplyr_1.1.4        tidyr_1.3.1        writexl_1.5.1      export_0.3.0       dittoSeq_1.14.3    ggplot2_3.5.1      BPCells_0.1.0     
 [8] Seurat_5.2.1       SeuratObject_5.0.2 sp_2.1-4          

loaded via a namespace (and not attached):
  [1] RcppAnnoy_0.0.22            splines_4.3.3               later_1.4.1                 bitops_1.0-9                tibble_3.2.1               
  [6] polyclip_1.10-7             fastDummies_1.7.4           lifecycle_1.0.4             globals_0.16.3              lattice_0.22-6             
 [11] MASS_7.3-60.0.1             backports_1.5.0             magrittr_2.0.3              openxlsx_4.2.7.1            plotly_4.10.4              
 [16] rmarkdown_2.29              httpuv_1.6.15               sctransform_0.4.1           spam_2.11-0                 zip_2.3.1                  
 [21] askpass_1.2.1               spatstat.sparse_3.1-0       reticulate_1.40.0           cowplot_1.1.3               pbapply_1.7-2              
 [26] RColorBrewer_1.1-3          pkgload_1.4.0               abind_1.4-8                 zlibbioc_1.48.2             Rtsne_0.17                 
 [31] GenomicRanges_1.54.1        purrr_1.0.2                 BiocGenerics_0.48.1         RCurl_1.98-1.16             rgl_1.3.17                 
 [36] gdtools_0.4.1               GenomeInfoDbData_1.2.11     IRanges_2.36.0              S4Vectors_0.40.2            ggrepel_0.9.6              
 [41] irlba_2.3.5.1               listenv_0.9.1               spatstat.utils_3.1-2        pheatmap_1.0.12             goftest_1.2-3              
 [46] RSpectra_0.16-2             spatstat.random_3.3-2       fitdistrplus_1.2-2          parallelly_1.41.0           codetools_0.2-20           
 [51] DelayedArray_0.28.0         xml2_1.3.6                  tidyselect_1.2.1            farver_2.1.2                base64enc_0.1-3            
 [56] matrixStats_1.5.0           stats4_4.3.3                spatstat.explore_3.3-4      jsonlite_1.8.9              progressr_0.15.1           
 [61] ggridges_0.5.6              survival_3.8-3              systemfonts_1.2.0           tools_4.3.3                 ragg_1.3.3                 
 [66] ica_1.0-3                   Rcpp_1.0.14                 glue_1.8.0                  gridExtra_2.3               SparseArray_1.2.4          
 [71] xfun_0.50                   MatrixGenerics_1.14.0       GenomeInfoDb_1.38.8         withr_3.0.2                 fastmap_1.2.0              
 [76] openssl_2.3.1               digest_0.6.37               R6_2.5.1                    mime_0.12                   textshaping_0.4.1          
 [81] colorspace_2.1-1            scattermore_1.2             tensor_1.5                  spatstat.data_3.1-4         generics_0.1.3             
 [86] fontLiberation_0.1.0        data.table_1.16.4           httr_1.4.7                  htmlwidgets_1.6.4           S4Arrays_1.2.1             
 [91] uwot_0.2.2                  pkgconfig_2.0.3             gtable_0.3.6                lmtest_0.9-40               SingleCellExperiment_1.24.0
 [96] XVector_0.42.0              htmltools_0.5.8.1           fontBitstreamVera_0.1.1     dotCall64_1.2               rvg_0.3.4                  
[101] scales_1.3.0                Biobase_2.62.0              png_0.1-8                   spatstat.univar_3.1-1       knitr_1.49                 
[106] rstudioapi_0.17.1           reshape2_1.4.4              uuid_1.2-1                  nlme_3.1-166                zoo_1.8-12                 
[111] flextable_0.9.7             stringr_1.5.1               KernSmooth_2.23-26          parallel_4.3.3              miniUI_0.1.1.1             
[116] pillar_1.10.1               grid_4.3.3                  vctrs_0.6.5                 RANN_2.6.2                  promises_1.3.2             
[121] xtable_1.8-4                cluster_2.1.8               evaluate_1.0.3              cli_3.6.3                   compiler_4.3.3             
[126] rlang_1.1.5                 crayon_1.5.3                future.apply_1.11.3         labeling_0.4.3              plyr_1.8.9                 
[131] stringi_1.8.4               viridisLite_0.4.2           deldir_2.0-4                munsell_0.5.1               lazyeval_0.2.2             
[136] spatstat.geom_3.3-5         fontquiver_0.2.1            Matrix_1.6-5                RcppHNSW_0.6.0              patchwork_1.3.0            
[141] future_1.34.0               devEMF_4.5                  stargazer_5.2.3             shiny_1.10.0                SummarizedExperiment_1.32.0
[146] ROCR_1.0-11                 igraph_2.1.3                broom_1.0.7                 officer_0.6.7              

Best
Stefan