Change of assay name in LengESCData

[PeteHaitch]

Sorry, another minor change in the non-legacy datasets, but noting in case someone else hits it.

suppressPackageStartupMessages(library(scRNAseq))

old <- LengESCData(legacy = TRUE)
#> see ?scRNAseq and browseVignettes('scRNAseq') for documentation
#> loading from cache
#> see ?scRNAseq and browseVignettes('scRNAseq') for documentation
#> loading from cache
new <- LengESCData()
assayNames(old)
#> [1] "normcounts"
assayNames(new)
#> [1] "normalized"

^{Created on 2024-04-18 with reprex v2.1.0}

Session info

sessionInfo()
#> R version 4.4.0 alpha (2024-04-02 r86304)
#> Platform: x86_64-pc-linux-gnu
#> Running under: Ubuntu 22.04.4 LTS
#> 
#> Matrix products: default
#> BLAS:   /home/peter/Downloads/R-alpha/lib/libRblas.so 
#> LAPACK: /home/peter/Downloads/R-alpha/lib/libRlapack.so;  LAPACK version 3.12.0
#> 
#> locale:
#>  [1] LC_CTYPE=en_AU.UTF-8       LC_NUMERIC=C              
#>  [3] LC_TIME=en_AU.UTF-8        LC_COLLATE=en_AU.UTF-8    
#>  [5] LC_MONETARY=en_AU.UTF-8    LC_MESSAGES=en_AU.UTF-8   
#>  [7] LC_PAPER=en_AU.UTF-8       LC_NAME=C                 
#>  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
#> [11] LC_MEASUREMENT=en_AU.UTF-8 LC_IDENTIFICATION=C       
#> 
#> time zone: Australia/Melbourne
#> tzcode source: system (glibc)
#> 
#> attached base packages:
#> [1] stats4    stats     graphics  grDevices utils     datasets  methods  
#> [8] base     
#> 
#> other attached packages:
#>  [1] scRNAseq_2.17.8             SingleCellExperiment_1.25.1
#>  [3] SummarizedExperiment_1.33.3 Biobase_2.63.1             
#>  [5] GenomicRanges_1.55.4        GenomeInfoDb_1.39.13       
#>  [7] IRanges_2.37.1              S4Vectors_0.41.6           
#>  [9] BiocGenerics_0.49.1         MatrixGenerics_1.15.0      
#> [11] matrixStats_1.3.0          
#> 
#> loaded via a namespace (and not attached):
#>  [1] DBI_1.2.2                bitops_1.0-7             httr2_1.0.1             
#>  [4] rlang_1.1.3              magrittr_2.0.3           gypsum_0.99.15          
#>  [7] compiler_4.4.0           RSQLite_2.3.6            GenomicFeatures_1.55.4  
#> [10] png_0.1-8                vctrs_0.6.5              ProtGenerics_1.35.4     
#> [13] pkgconfig_2.0.3          crayon_1.5.2             fastmap_1.1.1           
#> [16] dbplyr_2.5.0             XVector_0.43.1           utf8_1.2.4              
#> [19] Rsamtools_2.19.4         rmarkdown_2.26           UCSC.utils_0.99.5       
#> [22] purrr_1.0.2              bit_4.0.5                xfun_0.43               
#> [25] reprex_2.1.0             aws.s3_0.3.21            zlibbioc_1.49.3         
#> [28] cachem_1.0.8             jsonlite_1.8.8           blob_1.2.4              
#> [31] rhdf5filters_1.15.5      DelayedArray_0.29.9      Rhdf5lib_1.25.3         
#> [34] BiocParallel_1.37.1      parallel_4.4.0           R6_2.5.1                
#> [37] rtracklayer_1.63.2       Rcpp_1.0.12              knitr_1.46              
#> [40] base64enc_0.1-3          Matrix_1.7-0             tidyselect_1.2.1        
#> [43] abind_1.4-5              yaml_2.3.8               codetools_0.2-20        
#> [46] curl_5.2.1               lattice_0.22-6           alabaster.sce_1.3.3     
#> [49] tibble_3.2.1             withr_3.0.0              KEGGREST_1.43.0         
#> [52] evaluate_0.23            BiocFileCache_2.11.2     alabaster.schemas_1.3.1 
#> [55] xml2_1.3.6               ExperimentHub_2.11.1     Biostrings_2.71.5       
#> [58] pillar_1.9.0             BiocManager_1.30.22      filelock_1.0.3          
#> [61] generics_0.1.3           RCurl_1.98-1.14          BiocVersion_3.19.1      
#> [64] ensembldb_2.27.1         alabaster.base_1.3.23    alabaster.ranges_1.3.3  
#> [67] glue_1.7.0               alabaster.matrix_1.3.13  lazyeval_0.2.2          
#> [70] tools_4.4.0              AnnotationHub_3.11.4     BiocIO_1.13.0           
#> [73] GenomicAlignments_1.39.5 fs_1.6.3                 XML_3.99-0.16.1         
#> [76] rhdf5_2.47.7             grid_4.4.0               AnnotationDbi_1.65.2    
#> [79] GenomeInfoDbData_1.2.12  HDF5Array_1.31.6         restfulr_0.0.15         
#> [82] cli_3.6.2                rappdirs_0.3.3           fansi_1.0.6             
#> [85] S4Arrays_1.3.7           dplyr_1.1.4              AnnotationFilter_1.27.0 
#> [88] alabaster.se_1.3.4       digest_0.6.35            SparseArray_1.3.5       
#> [91] rjson_0.2.21             memoise_2.0.1            htmltools_0.5.8.1       
#> [94] lifecycle_1.0.4          httr_1.4.7               mime_0.12               
#> [97] aws.signature_0.6.0      bit64_4.0.5

[LTLA]

Oops. Not sure whether it was intentional, maybe I was trying to standardize all non-counts assay names. But reading the GEO description does indicate that the matrix does indeed contain normalized counts, so I've put it back in 2.17.9.

[PeteHaitch]

Thanks, Aaron!