Change of assay name in LengESCData
PeteHaitch opened this issue · comments
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
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.
Thanks, Aaron!