Error getting gene regions from Homo.sapiens

[lmckinno]

Hello, can you help me make sense of this error? I am trying to get the gene regions from Homo.sapiens but I am having trouble with it dropping genes and can't find a way around it. Thanks!

regions <- genes(Homo.sapiens,columns=c("SYMBOL","GENEID"))
1655 genes were dropped because they have exons located on both strands of the same
reference sequence or on more than one reference sequence, so cannot be represented by a
single genomic range.
Use 'single.strand.genes.only=FALSE' to get all the genes in a GRangesList object, or
use suppressMessages() to suppress this message.
'select()' returned 1:1 mapping between keys and columns

regions <- genes(Homo.sapiens,columns=c("SYMBOL","GENEID"),single.strand.genes.only=FALSE)
Error in .local(x, ...) :
unused argument (single.strand.genes.only = FALSE)

[jorainer]

Can you please provide some more information? what is Homo.sapiens and how did you create that variable? Also, please provide the output of your sessionInfo() so that I can check which version of R and ensembldb you are using.

[lmckinno]

Yes, thank you!

Homo.sapiens came from the R package which I loaded using library(Homo.sapiens).

sessionInfo()
R version 4.1.0 (2021-05-18)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 8

Matrix products: default
BLAS/LAPACK: /usr/lib64/libopenblasp-r0.3.12.so

locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8
[4] LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats4 stats graphics grDevices utils datasets methods base

other attached packages:
[1] Homo.sapiens_1.3.1 TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2
[3] org.Hs.eg.db_3.14.0 GO.db_3.14.0
[5] OrganismDbi_1.36.0 TxDb.Hsapiens.UCSC.hg38.knownGene_3.14.0
[7] ensembldb_2.18.4 GenomicFeatures_1.46.5
[9] AnnotationDbi_1.56.2 Biobase_2.54.0
[11] GenomicDataCommons_1.23.2 magrittr_2.0.2
[13] stringr_1.4.0 TFBSTools_1.32.0
[15] gmapR_1.36.0 Rsamtools_2.10.0
[17] Biostrings_2.62.0 XVector_0.34.0
[19] GenomicRanges_1.46.1 GenomeInfoDb_1.30.1
[21] IRanges_2.28.0 S4Vectors_0.32.3
[23] BiocGenerics_0.40.0 SeuratObject_4.0.4
[25] AnnotationFilter_1.18.0

loaded via a namespace (and not attached):
[1] utf8_1.2.2 R.utils_2.11.0 tidyselect_1.1.2
[4] poweRlaw_0.70.6 RSQLite_2.2.11 htmlwidgets_1.5.4
[7] grid_4.1.0 BiocParallel_1.28.3 scatterpie_0.1.7
[10] munsell_0.5.0 codetools_0.2-18 systemPipeR_2.0.8
[13] colorspace_2.0-3 GOSemSim_2.20.0 filelock_1.0.2
[16] rstudioapi_0.13 DOSE_3.20.1 MatrixGenerics_1.6.0
[19] bbmle_1.0.24 GenomeInfoDbData_1.2.7 mixsqp_0.3-43
[22] hwriter_1.3.2.1 polyclip_1.10-0 bit64_4.0.5
[25] farver_2.1.0 downloader_0.4 coda_0.19-4
[28] vctrs_0.3.8 treeio_1.18.1 generics_0.1.2
[31] BiocFileCache_2.2.1 R6_2.5.1 doParallel_1.0.17
[34] clue_0.3-60 apeglm_1.16.0 graphlayouts_0.8.0
[37] invgamma_1.1 locfit_1.5-9.5 bitops_1.0-7
[40] cachem_1.0.6 fgsea_1.20.0 gridGraphics_0.5-1
[43] DelayedArray_0.20.0 assertthat_0.2.1 BiocIO_1.4.0
[46] scales_1.1.1 ggraph_2.0.5 enrichplot_1.14.2
[49] gtable_0.3.0 tidygraph_1.2.1 seqLogo_1.60.0
[52] rlang_1.1.0 GlobalOptions_0.1.2 splines_4.1.0
[55] rtracklayer_1.54.0 lazyeval_0.2.2 BiocManager_1.30.16
[58] yaml_2.3.5 reshape2_1.4.4 DiffBind_3.4.11
[61] qvalue_2.26.0 RBGL_1.70.0 clusterProfiler_4.2.2
[64] tools_4.1.0 ggplotify_0.1.0 ggplot2_3.3.5
[67] ellipsis_0.3.2 gplots_3.1.3 RColorBrewer_1.1-2
[70] Rcpp_1.0.8.3 plyr_1.8.6 progress_1.2.2
[73] zlibbioc_1.40.0 purrr_0.3.4 RCurl_1.98-1.6
[76] prettyunits_1.1.1 VariantTools_1.36.0 GetoptLong_1.0.5
[79] viridis_0.6.2 ashr_2.2-54 SummarizedExperiment_1.24.0
[82] ggrepel_0.9.1 cluster_2.1.2 data.table_1.14.2
[85] DO.db_2.9 circlize_0.4.14 truncnorm_1.0-8
[88] SQUAREM_2021.1 mvtnorm_1.1-3 amap_0.8-18
[91] ProtGenerics_1.26.0 matrixStats_0.61.0 xtable_1.8-4
[94] hms_1.1.1 patchwork_1.1.1 XML_3.99-0.9
[97] emdbook_1.3.12 jpeg_0.1-9 gridExtra_2.3
[100] shape_1.4.6 compiler_4.1.0 biomaRt_2.50.3
[103] bdsmatrix_1.3-4 tibble_3.1.6 KernSmooth_2.23-20
[106] crayon_1.5.0 shadowtext_0.1.2 R.oo_1.24.0
[109] htmltools_0.5.2 tzdb_0.2.0 ggfun_0.0.6
[112] tidyr_1.2.0 aplot_0.1.3 DBI_1.1.2
[115] tweenr_1.0.2 dbplyr_2.1.1 ComplexHeatmap_2.10.0
[118] MASS_7.3-56 rappdirs_0.3.3 readr_2.1.2
[121] ShortRead_1.52.0 Matrix_1.4-1 cli_3.6.1
[124] R.methodsS3_1.8.1 parallel_4.1.0 igraph_1.3.1
[127] pkgconfig_2.0.3 TFMPvalue_0.0.8 GenomicAlignments_1.30.0
[130] numDeriv_2016.8-1.1 xml2_1.3.3 foreach_1.5.2
[133] annotate_1.72.0 ggtree_3.2.1 DirichletMultinomial_1.36.0
[136] yulab.utils_0.0.4 VariantAnnotation_1.40.0 digest_0.6.29
[139] pracma_2.3.8 CNEr_1.30.0 graph_1.72.0
[142] fastmatch_1.1-3 tidytree_0.3.9 GreyListChIP_1.26.0
[145] restfulr_0.0.13 curl_4.3.2 gtools_3.9.2
[148] rjson_0.2.21 lifecycle_1.0.1 nlme_3.1-155
[151] jsonlite_1.8.0 viridisLite_0.4.0 limma_3.50.1
[154] BSgenome_1.62.0 fansi_1.0.3 pillar_1.7.0
[157] lattice_0.20-45 KEGGREST_1.34.0 fastmap_1.1.0
[160] httr_1.4.2 glue_1.6.2 png_0.1-7
[163] iterators_1.0.14 bit_4.0.4 ggforce_0.3.3
[166] stringi_1.7.6 blob_1.2.2 latticeExtra_0.6-29
[169] caTools_1.18.2 memoise_2.0.1 dplyr_1.0.8
[172] irlba_2.3.5 ape_5.6-2

[jorainer]

Homo.sapiens is a OrganismDb package - so, there is not much I can do to help since this is not related with ensembldb. Maybe best to ask this question on the Bioconductor support site?