Skip to content

no exprs function exported from flowWorkspace #407

@SamGG

Description

@SamGG

Describe the bug
I can use the method exprs on a cytoframe

To Reproduce

dataDir <- system.file("extdata",package="flowWorkspaceData")
files <- list.files(dataDir, "Cyto", full.names = TRUE)
library(flowWorkspace)
#> As part of improvements to flowWorkspace, some behavior of
#> GatingSet objects has changed. For details, please read the section
#> titled "The cytoframe and cytoset classes" in the package vignette:
#> 
#>   vignette("flowWorkspace-Introduction", "flowWorkspace")
cf <- load_cytoframe_from_fcs(files[1], num_threads = 4)
cf
#> cytoframe object 'CytoTrol_CytoTrol_1.fcs'
#> with 119531 cells and 12 observables:
#>        name         desc     range  minRange  maxRange
#> $P1   FSC-A           NA    262143         0    262143
#> $P2   FSC-H           NA    262143         0    262143
#> $P3   FSC-W           NA    262143         0    262143
#> $P4   SSC-A           NA    262143         0    262143
#> $P5  B710-A  CD4 PcpCy55    262143      -111    262143
#> ...     ...          ...       ...       ...       ...
#> $P8  V450-A     CD3 V450    262143      -111    262143
#> $P9  V545-A  HLA-DR V500    262143      -111    262143
#> $P10 G560-A      CCR7 PE    262143      -111    262143
#> $P11 G780-A CD45RA PECy7    262143      -111    262143
#> $P12   Time           NA    262143         0    262143
#> 199 keywords are stored in the 'description' slot
#> row names(0):
exprs(cf)
#> Error in `exprs()`:
#> ! could not find function "exprs"
sessionInfo()
#> R version 4.5.2 (2025-10-31 ucrt)
#> Platform: x86_64-w64-mingw32/x64
#> Running under: Windows 11 x64 (build 26200)
#> 
#> Matrix products: default
#>   LAPACK version 3.12.1
#> 
#> locale:
#> [1] LC_COLLATE=French_France.utf8  LC_CTYPE=French_France.utf8   
#> [3] LC_MONETARY=French_France.utf8 LC_NUMERIC=C                  
#> [5] LC_TIME=French_France.utf8    
#> 
#> time zone: Europe/Paris
#> tzcode source: internal
#> 
#> attached base packages:
#> [1] stats     graphics  grDevices utils     datasets  methods   base     
#> 
#> other attached packages:
#> [1] flowWorkspace_4.22.1
#> 
#> loaded via a namespace (and not attached):
#>  [1] Matrix_1.7-4          dplyr_1.2.0           compiler_4.5.2       
#>  [4] reprex_2.1.1          tidyselect_1.2.1      Biobase_2.70.0       
#>  [7] cytolib_2.22.0        Rgraphviz_2.54.0      IRanges_2.44.0       
#> [10] scales_1.4.0          yaml_2.3.12           fastmap_1.2.0        
#> [13] lattice_0.22-9        XVector_0.50.0        R6_2.6.1             
#> [16] RProtoBufLib_2.22.0   S4Arrays_1.10.1       generics_0.1.4       
#> [19] knitr_1.51            BiocGenerics_0.56.0   XML_3.99-0.22        
#> [22] graph_1.88.1          DelayedArray_0.36.0   tibble_3.3.1         
#> [25] MatrixGenerics_1.22.0 RColorBrewer_1.1-3    pillar_1.11.1        
#> [28] ncdfFlow_2.56.0       rlang_1.1.7           flowCore_2.22.1      
#> [31] xfun_0.56             fs_1.6.6              otel_0.2.0           
#> [34] SparseArray_1.10.8    cli_3.6.5             withr_3.0.2          
#> [37] magrittr_2.0.4        digest_0.6.39         grid_4.5.2           
#> [40] rstudioapi_0.18.0     lifecycle_1.0.5       S4Vectors_0.48.0     
#> [43] vctrs_0.7.1           evaluate_1.0.5        glue_1.8.0           
#> [46] data.table_1.18.2.1   farver_2.1.2          abind_1.4-8          
#> [49] stats4_4.5.2          rmarkdown_2.30        matrixStats_1.5.0    
#> [52] tools_4.5.2           pkgconfig_2.0.3       htmltools_0.5.9

Created on 2026-04-17 with reprex v2.1.1

Expected behavior
I should view the expression intensities.

Additional context
The previous code is working if flowCore is loaded, but doing so makes me unclear of the underlying transformation: the cytoframe is converted to a flowFrame, then exprs is applied?

Metadata

Metadata

Assignees

No one assigned

    Labels

    No labels
    No labels

    Type

    No type

    Projects

    No projects

    Milestone

    No milestone

    Relationships

    None yet

    Development

    No branches or pull requests

    Issue actions