SingleCellExperiment
SingleCellExperiment copied to clipboard
drisso
Coercion from *SingleCellExperiment* to *SummarizedExperiment* loses rownames
suppressPackageStartupMessages(library(SingleCellExperiment))
example(SingleCellExperiment, echo = FALSE)
rownames(sce) <- paste0("Gene_", seq_len(nrow(sce)))
# Coercion loses rownames of rowData.
rownames(sce)
#> [1] "Gene_1" "Gene_2" "Gene_3" "Gene_4" "Gene_5" "Gene_6"
#> [7] "Gene_7" "Gene_8" "Gene_9" "Gene_10" "Gene_11" "Gene_12"
#> [13] "Gene_13" "Gene_14" "Gene_15" "Gene_16" "Gene_17" "Gene_18"
#> [19] "Gene_19" "Gene_20" "Gene_21" "Gene_22" "Gene_23" "Gene_24"
#> [25] "Gene_25" "Gene_26" "Gene_27" "Gene_28" "Gene_29" "Gene_30"
#> [31] "Gene_31" "Gene_32" "Gene_33" "Gene_34" "Gene_35" "Gene_36"
#> [37] "Gene_37" "Gene_38" "Gene_39" "Gene_40" "Gene_41" "Gene_42"
#> [43] "Gene_43" "Gene_44" "Gene_45" "Gene_46" "Gene_47" "Gene_48"
#> [49] "Gene_49" "Gene_50" "Gene_51" "Gene_52" "Gene_53" "Gene_54"
#> [55] "Gene_55" "Gene_56" "Gene_57" "Gene_58" "Gene_59" "Gene_60"
#> [61] "Gene_61" "Gene_62" "Gene_63" "Gene_64" "Gene_65" "Gene_66"
#> [67] "Gene_67" "Gene_68" "Gene_69" "Gene_70" "Gene_71" "Gene_72"
#> [73] "Gene_73" "Gene_74" "Gene_75" "Gene_76" "Gene_77" "Gene_78"
#> [79] "Gene_79" "Gene_80" "Gene_81" "Gene_82" "Gene_83" "Gene_84"
#> [85] "Gene_85" "Gene_86" "Gene_87" "Gene_88" "Gene_89" "Gene_90"
#> [91] "Gene_91" "Gene_92" "Gene_93" "Gene_94" "Gene_95" "Gene_96"
#> [97] "Gene_97" "Gene_98" "Gene_99" "Gene_100" "Gene_101" "Gene_102"
#> [103] "Gene_103" "Gene_104" "Gene_105" "Gene_106" "Gene_107" "Gene_108"
#> [109] "Gene_109" "Gene_110" "Gene_111" "Gene_112" "Gene_113" "Gene_114"
#> [115] "Gene_115" "Gene_116" "Gene_117" "Gene_118" "Gene_119" "Gene_120"
#> [121] "Gene_121" "Gene_122" "Gene_123" "Gene_124" "Gene_125" "Gene_126"
#> [127] "Gene_127" "Gene_128" "Gene_129" "Gene_130" "Gene_131" "Gene_132"
#> [133] "Gene_133" "Gene_134" "Gene_135" "Gene_136" "Gene_137" "Gene_138"
#> [139] "Gene_139" "Gene_140" "Gene_141" "Gene_142" "Gene_143" "Gene_144"
#> [145] "Gene_145" "Gene_146" "Gene_147" "Gene_148" "Gene_149" "Gene_150"
#> [151] "Gene_151" "Gene_152" "Gene_153" "Gene_154" "Gene_155" "Gene_156"
#> [157] "Gene_157" "Gene_158" "Gene_159" "Gene_160" "Gene_161" "Gene_162"
#> [163] "Gene_163" "Gene_164" "Gene_165" "Gene_166" "Gene_167" "Gene_168"
#> [169] "Gene_169" "Gene_170" "Gene_171" "Gene_172" "Gene_173" "Gene_174"
#> [175] "Gene_175" "Gene_176" "Gene_177" "Gene_178" "Gene_179" "Gene_180"
#> [181] "Gene_181" "Gene_182" "Gene_183" "Gene_184" "Gene_185" "Gene_186"
#> [187] "Gene_187" "Gene_188" "Gene_189" "Gene_190" "Gene_191" "Gene_192"
#> [193] "Gene_193" "Gene_194" "Gene_195" "Gene_196" "Gene_197" "Gene_198"
#> [199] "Gene_199" "Gene_200"
rownames(as(sce, "SummarizedExperiment"))
#> NULL
# It seems the loss occurs from the rowData slot?
rownames(rowData(sce))
#> [1] "Gene_1" "Gene_2" "Gene_3" "Gene_4" "Gene_5" "Gene_6"
#> [7] "Gene_7" "Gene_8" "Gene_9" "Gene_10" "Gene_11" "Gene_12"
#> [13] "Gene_13" "Gene_14" "Gene_15" "Gene_16" "Gene_17" "Gene_18"
#> [19] "Gene_19" "Gene_20" "Gene_21" "Gene_22" "Gene_23" "Gene_24"
#> [25] "Gene_25" "Gene_26" "Gene_27" "Gene_28" "Gene_29" "Gene_30"
#> [31] "Gene_31" "Gene_32" "Gene_33" "Gene_34" "Gene_35" "Gene_36"
#> [37] "Gene_37" "Gene_38" "Gene_39" "Gene_40" "Gene_41" "Gene_42"
#> [43] "Gene_43" "Gene_44" "Gene_45" "Gene_46" "Gene_47" "Gene_48"
#> [49] "Gene_49" "Gene_50" "Gene_51" "Gene_52" "Gene_53" "Gene_54"
#> [55] "Gene_55" "Gene_56" "Gene_57" "Gene_58" "Gene_59" "Gene_60"
#> [61] "Gene_61" "Gene_62" "Gene_63" "Gene_64" "Gene_65" "Gene_66"
#> [67] "Gene_67" "Gene_68" "Gene_69" "Gene_70" "Gene_71" "Gene_72"
#> [73] "Gene_73" "Gene_74" "Gene_75" "Gene_76" "Gene_77" "Gene_78"
#> [79] "Gene_79" "Gene_80" "Gene_81" "Gene_82" "Gene_83" "Gene_84"
#> [85] "Gene_85" "Gene_86" "Gene_87" "Gene_88" "Gene_89" "Gene_90"
#> [91] "Gene_91" "Gene_92" "Gene_93" "Gene_94" "Gene_95" "Gene_96"
#> [97] "Gene_97" "Gene_98" "Gene_99" "Gene_100" "Gene_101" "Gene_102"
#> [103] "Gene_103" "Gene_104" "Gene_105" "Gene_106" "Gene_107" "Gene_108"
#> [109] "Gene_109" "Gene_110" "Gene_111" "Gene_112" "Gene_113" "Gene_114"
#> [115] "Gene_115" "Gene_116" "Gene_117" "Gene_118" "Gene_119" "Gene_120"
#> [121] "Gene_121" "Gene_122" "Gene_123" "Gene_124" "Gene_125" "Gene_126"
#> [127] "Gene_127" "Gene_128" "Gene_129" "Gene_130" "Gene_131" "Gene_132"
#> [133] "Gene_133" "Gene_134" "Gene_135" "Gene_136" "Gene_137" "Gene_138"
#> [139] "Gene_139" "Gene_140" "Gene_141" "Gene_142" "Gene_143" "Gene_144"
#> [145] "Gene_145" "Gene_146" "Gene_147" "Gene_148" "Gene_149" "Gene_150"
#> [151] "Gene_151" "Gene_152" "Gene_153" "Gene_154" "Gene_155" "Gene_156"
#> [157] "Gene_157" "Gene_158" "Gene_159" "Gene_160" "Gene_161" "Gene_162"
#> [163] "Gene_163" "Gene_164" "Gene_165" "Gene_166" "Gene_167" "Gene_168"
#> [169] "Gene_169" "Gene_170" "Gene_171" "Gene_172" "Gene_173" "Gene_174"
#> [175] "Gene_175" "Gene_176" "Gene_177" "Gene_178" "Gene_179" "Gene_180"
#> [181] "Gene_181" "Gene_182" "Gene_183" "Gene_184" "Gene_185" "Gene_186"
#> [187] "Gene_187" "Gene_188" "Gene_189" "Gene_190" "Gene_191" "Gene_192"
#> [193] "Gene_193" "Gene_194" "Gene_195" "Gene_196" "Gene_197" "Gene_198"
#> [199] "Gene_199" "Gene_200"
rownames(rowData(as(sce, "SummarizedExperiment")))
#> NULL
Created on 2022-01-12 by the reprex package (v2.0.1)
Session info
sessioninfo::session_info()
#> ─ Session info ───────────────────────────────────────────────────────────────
#> setting value
#> version R version 4.1.2 (2021-11-01)
#> os Ubuntu 20.04.3 LTS
#> system x86_64, linux-gnu
#> ui X11
#> language en_AU:en
#> collate en_AU.UTF-8
#> ctype en_AU.UTF-8
#> tz Australia/Melbourne
#> date 2022-01-12
#> pandoc 2.11.4 @ /usr/lib/rstudio/bin/pandoc/ (via rmarkdown)
#>
#> ─ Packages ───────────────────────────────────────────────────────────────────
#> package * version date (UTC) lib source
#> Biobase * 2.54.0 2021-10-26 [1] RSPM (R 4.1.2)
#> BiocGenerics * 0.40.0 2021-10-26 [1] RSPM (R 4.1.2)
#> bitops 1.0-7 2021-04-24 [1] RSPM (R 4.1.0)
#> cli 3.1.0 2021-10-27 [1] RSPM (R 4.1.2)
#> DelayedArray 0.20.0 2021-10-26 [1] RSPM (R 4.1.2)
#> digest 0.6.29 2021-12-01 [1] RSPM (R 4.1.2)
#> evaluate 0.14 2019-05-28 [1] RSPM (R 4.1.0)
#> fastmap 1.1.0 2021-01-25 [1] RSPM (R 4.1.0)
#> fs 1.5.2 2021-12-08 [1] RSPM (R 4.1.2)
#> GenomeInfoDb * 1.30.0 2021-10-26 [1] RSPM (R 4.1.2)
#> GenomeInfoDbData 1.2.7 2021-10-28 [1] RSPM (R 4.1.1)
#> GenomicRanges * 1.46.1 2021-11-18 [1] RSPM (R 4.1.2)
#> glue 1.6.0 2021-12-17 [1] RSPM (R 4.1.0)
#> highr 0.9 2021-04-16 [1] RSPM (R 4.1.0)
#> htmltools 0.5.2 2021-08-25 [1] RSPM (R 4.1.0)
#> IRanges * 2.28.0 2021-10-26 [1] RSPM (R 4.1.2)
#> knitr 1.37 2021-12-16 [1] RSPM (R 4.1.0)
#> lattice 0.20-45 2021-09-22 [4] CRAN (R 4.1.1)
#> magrittr 2.0.1 2020-11-17 [1] RSPM (R 4.1.0)
#> Matrix 1.4-0 2021-12-08 [4] CRAN (R 4.1.2)
#> MatrixGenerics * 1.6.0 2021-10-26 [1] RSPM (R 4.1.2)
#> matrixStats * 0.61.0 2021-09-17 [1] RSPM (R 4.1.1)
#> RCurl 1.98-1.5 2021-09-17 [1] RSPM (R 4.1.1)
#> reprex 2.0.1 2021-08-05 [1] RSPM (R 4.1.0)
#> rlang 0.4.12 2021-10-18 [1] RSPM (R 4.1.1)
#> rmarkdown 2.11 2021-09-14 [1] RSPM (R 4.1.1)
#> rstudioapi 0.13 2020-11-12 [1] RSPM (R 4.1.0)
#> S4Vectors * 0.32.3 2021-11-21 [1] RSPM (R 4.1.2)
#> sessioninfo 1.2.2 2021-12-06 [1] RSPM (R 4.1.2)
#> SingleCellExperiment * 1.16.0 2021-10-26 [1] RSPM (R 4.1.2)
#> stringi 1.7.6 2021-11-29 [1] RSPM (R 4.1.2)
#> stringr 1.4.0 2019-02-10 [1] RSPM (R 4.1.0)
#> SummarizedExperiment * 1.24.0 2021-10-26 [1] RSPM (R 4.1.2)
#> withr 2.4.3 2021-11-30 [1] RSPM (R 4.1.2)
#> xfun 0.29 2021-12-14 [1] RSPM (R 4.1.0)
#> XVector 0.34.0 2021-10-26 [1] RSPM (R 4.1.2)
#> yaml 2.2.1 2020-02-01 [1] RSPM (R 4.1.0)
#> zlibbioc 1.40.0 2021-10-26 [1] RSPM (R 4.1.2)
#>
#> [1] /home/peter/R/x86_64-pc-linux-gnu-library/4.1
#> [2] /usr/local/lib/R/site-library
#> [3] /usr/lib/R/site-library
#> [4] /usr/lib/R/library
#>
#> ──────────────────────────────────────────────────────────────────────────────
Oh I now see https://github.com/Bioconductor/SummarizedExperiment/issues/29.