subsetArchRProject fails during barcode collisions between samples

[dgodovich]

Hello,

When using subsetArchRProject to subset by cells, I noticed that if I used the resulting ArrowFiles there were more cells than I expected. After investigating, I found that this was caused by repeated 10X barcodes between samples - these had unique cell names of the form [sample]#[barcode], but this information is stripped when the ArrowFiles are copied over (see this line of code).

Current behavior: ArrowFiles are subsetted to any cells that have matching barcodes, even if that is between samples.
Expected behavior: ArrowFiles are subsetted to exactly the cells you specify

See below for a reproducible example with the tutorial dataset.

library(ArchR)
library(parallel)
inputFiles <- getTutorialData("Hematopoiesis")
addArchRGenome("hg19")
addArchRThreads(threads = 16) 

ArrowFiles <- createArrowFiles(
  inputFiles = inputFiles,
  sampleNames = names(inputFiles),
  minTSS = 4,
  minFrags = 1000, 
  addTileMat = FALSE,
  addGeneScoreMat = FALSE
)

projHeme1 <- ArchRProject(
  ArrowFiles = ArrowFiles, 
  outputDirectory = "HemeTutorial",
  copyArrows = TRUE
)

barcodes <- sapply(strsplit(getCellNames(projHeme1),'#'), '[')[2,]
cell_subset <- getCellNames(projHeme1)[barcodes %>% duplicated(fromLast = TRUE)]
print(length(cell_subset)) # 43

projSubset <- subsetArchRProject(
    ArchRProj = projHeme1,
    cells = cell_subset,
    outputDirectory = "ArchRSubset",
    dropCells = TRUE,
    force = TRUE
)

print(nCells(projSubset)) # has the expected 43 cells

print(lapply(getArrowFiles(projSubset), nCells) %>% unlist %>% sum) # 70
# ArrowFiles of this project have 70 cells

test_subset <- ArchRProject(getArrowFiles(projSubset), outputDirectory = 'test_proj/')
print(nCells(test_subset))
# also has 70 cells

sessionInfo()

R version 4.3.2 (2023-10-31)
Platform: x86_64-conda-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS/LAPACK: /lila/home/godovid/miniconda3/envs/workshop_2024/lib/libopenblasp-r0.3.25.so;  LAPACK version 3.11.0

Random number generation:
 RNG:     L'Ecuyer-CMRG 
 Normal:  Inversion 
 Sample:  Rejection 
 
locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

time zone: America/New_York
tzcode source: system (glibc)

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

other attached packages:
 [1] BSgenome.Hsapiens.UCSC.hg19_1.4.3 BSgenome_1.70.2                  
 [3] rtracklayer_1.62.0                BiocIO_1.12.0                    
 [5] Biostrings_2.70.3                 XVector_0.42.0                   
 [7] rhdf5_2.46.1                      SummarizedExperiment_1.32.0      
 [9] Biobase_2.62.0                    RcppArmadillo_0.12.8.3.0         
[11] Rcpp_1.0.13                       Matrix_1.6-5                     
[13] GenomicRanges_1.54.1              GenomeInfoDb_1.38.8              
[15] IRanges_2.36.0                    S4Vectors_0.40.2                 
[17] BiocGenerics_0.48.1               sparseMatrixStats_1.14.0         
[19] MatrixGenerics_1.14.0             matrixStats_1.3.0                
[21] data.table_1.15.4                 stringr_1.5.1                    
[23] plyr_1.8.9                        magrittr_2.0.3                   
[25] ggplot2_3.5.1                     gtable_0.3.5                     
[27] gtools_3.9.5                      gridExtra_2.3                    
[29] devtools_2.4.5                    usethis_2.2.2                    
[31] ArchR_1.0.3                      

loaded via a namespace (and not attached):
 [1] bitops_1.0-7             remotes_2.4.2.1          rlang_1.1.4             
 [4] compiler_4.3.2           callr_3.7.3              vctrs_0.6.5             
 [7] profvis_0.3.8            pkgconfig_2.0.3          crayon_1.5.2            
[10] fastmap_1.2.0            ellipsis_0.3.2           utf8_1.2.4              
[13] Rsamtools_2.18.0         promises_1.3.0           sessioninfo_1.2.2       
[16] ps_1.7.6                 purrr_1.0.2              zlibbioc_1.48.2         
[19] cachem_1.0.8             jsonlite_1.8.8           later_1.3.2             
[22] rhdf5filters_1.14.1      DelayedArray_0.28.0      BiocParallel_1.36.0     
[25] uuid_1.2-0               Rhdf5lib_1.24.2          prettyunits_1.2.0       
[28] R6_2.5.1                 stringi_1.8.4            pkgload_1.3.4           
[31] IRkernel_1.3.2           base64enc_0.1-3          httpuv_1.6.15           
[34] tidyselect_1.2.1         yaml_2.3.8               abind_1.4-5             
[37] codetools_0.2-19         miniUI_0.1.1.1           processx_3.8.3          
[40] pkgbuild_1.4.2           lattice_0.22-5           tibble_3.2.1            
[43] shiny_1.8.1.1            withr_3.0.1              evaluate_0.23           
[46] urlchecker_1.0.1         pillar_1.9.0             generics_0.1.3          
[49] RCurl_1.98-1.14          IRdisplay_1.1            munsell_0.5.1           
[52] scales_1.3.0             xtable_1.8-4             glue_1.7.0              
[55] tools_4.3.2              GenomicAlignments_1.38.2 pbdZMQ_0.3-11           
[58] fs_1.6.4                 XML_3.99-0.16.1          colorspace_2.1-1        
[61] GenomeInfoDbData_1.2.11  repr_1.1.7               restfulr_0.0.15         
[64] cli_3.6.3                fansi_1.0.6              S4Arrays_1.2.1          
[67] dplyr_1.1.4              digest_0.6.35            SparseArray_1.2.4       
[70] rjson_0.2.21             htmlwidgets_1.6.4        memoise_2.0.1           
[73] htmltools_0.5.8.1        lifecycle_1.0.4          mime_0.12               

[immanuelazn]

Hi @dgodovich! Thanks for using ArchR! Please make sure that your post belongs in the Issues section. Only bugs and error reports belong in the Issues section. Usage questions and feature requests should be posted in the Discussions section, not in Issues.

If you are getting an error, it is likely due to something specific to your dataset, usage, or computational environment, all of which are extremely challenging to troubleshoot. As such, we require reproducible examples (preferably using the tutorial dataset) from users who want assistance. If you cannot reproduce your error, we will not be able to help.
Before going through the work of making a reproducible example, search the previous Issues, Discussions, function definitions, or the ArchR manual and you will likely find the answers you are looking for.
If your post does not contain a reproducible example, it is unlikely to receive a response.

In addition to a reproducible example, you must do the following things before we help you, unless your original post already contained this information:
1. If you've encountered an error, have you already searched previous Issues to make sure that this hasn't already been solved?
2. Did you post your log file? If not, add it now.
3. Remove any screenshots that contain text and instead copy and paste the text using markdown's codeblock syntax (three consecutive backticks). You can do this by editing your original post.

[dgodovich]

Hey,

Looking further down in the .copyArrowSingle function, I saw that other cellName assignments were sample aware (e.g. here), so I changed the line mentioned above to have a similar format. I created a pull request to merge this change.