issue with Ensembl
Hi there,
I am trying to get the gene name using this code
libreNameEnsembl <- as.matrix(cds@rowRanges@elementMetadata@listData$gene_short_name)
GeneNameSymbol <- AnnotationDbi::select(org.Mm.eg.db, keys=GeneNameEnsembl, columns='SYMBOL', keytype='ENSEMBL')
but I keep getting this error:
Error in .testForValidKeys(x, keys, keytype, fks) :
object 'GeneNameEnsembl' not found
> sessionInfo()
R version 4.2.2 (2022-10-31)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS Monterey 12.1
Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRlapack.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats4 stats graphics grDevices
[5] utils datasets methods base
other attached packages:
[1] Hmisc_4.7-2
[2] Formula_1.2-4
[3] survival_3.4-0
[4] lattice_0.20-45
[5] org.Mm.eg.db_3.16.0
[6] AnnotationDbi_1.60.0
[7] Matrix_1.5-3
[8] reticulate_1.26
[9] dplyr_1.0.10
[10] magrittr_2.0.3
[11] ggplot2_3.4.0
[12] monocle3_1.3.1
[13] SingleCellExperiment_1.20.0
[14] SummarizedExperiment_1.28.0
[15] GenomicRanges_1.50.2
[16] GenomeInfoDb_1.34.6
[17] IRanges_2.32.0
[18] S4Vectors_0.36.1
[19] MatrixGenerics_1.10.0
[20] matrixStats_0.63.0
[21] Biobase_2.58.0
[22] BiocGenerics_0.44.0
loaded via a namespace (and not attached):
[1] nlme_3.1-161 bitops_1.0-7
[3] bit64_4.0.5 RColorBrewer_1.1-3
[5] httr_1.4.4 backports_1.4.1
[7] tools_4.2.2 utf8_1.2.2
[9] R6_2.5.1 rpart_4.1.19
[11] DBI_1.1.3 colorspace_2.0-3
[13] nnet_7.3-18 withr_2.5.0
[15] tidyselect_1.2.0 gridExtra_2.3
[17] bit_4.0.5 compiler_4.2.2
[19] cli_3.5.0 htmlTable_2.4.1
[21] DelayedArray_0.24.0 scales_1.2.1
[23] checkmate_2.1.0 stringr_1.5.0
[25] digest_0.6.31 foreign_0.8-84
[27] minqa_1.2.5 XVector_0.38.0
[29] htmltools_0.5.4 base64enc_0.1-3
[31] jpeg_0.1-10 pkgconfig_2.0.3
[33] parallelly_1.33.0 lme4_1.1-31
[35] fastmap_1.1.0 htmlwidgets_1.6.0
[37] rlang_1.0.6 rstudioapi_0.14
[39] RSQLite_2.2.20 generics_0.1.3
[41] jsonlite_1.8.4 RCurl_1.98-1.9
[43] GenomeInfoDbData_1.2.9 interp_1.1-3
[45] Rcpp_1.0.9 munsell_0.5.0
[47] fansi_1.0.3 lifecycle_1.0.3
[49] terra_1.6-47 stringi_1.7.8
[51] MASS_7.3-58.1 zlibbioc_1.44.0
[53] plyr_1.8.8 grid_4.2.2
[55] blob_1.2.3 parallel_4.2.2
[57] listenv_0.9.0 crayon_1.5.2
[59] deldir_1.0-6 Biostrings_2.66.0
[61] splines_4.2.2 KEGGREST_1.38.0
[63] knitr_1.41 pillar_1.8.1
[65] igraph_1.3.5 boot_1.3-28.1
[67] codetools_0.2-18 glue_1.6.2
[69] latticeExtra_0.6-30 data.table_1.14.6
[71] png_0.1-8 vctrs_0.5.1
[73] nloptr_2.0.3 gtable_0.3.1
[75] future_1.30.0 assertthat_0.2.1
[77] cachem_1.0.6 xfun_0.36
[79] tibble_3.1.8 memoise_2.0.1
[81] cluster_2.1.4 globals_0.16.2
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1 answer
Try keys = "GeneNameEnsembl". Quoting something should be your second thought when you see the object not found error. The first would be to make sure you don't expect the object to exist as an object.
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