No 'TxDb.Hsapiens.UCSC.hg38.knownGene' object
1
@user-24831
Last seen 3.7 years ago
During my genome analysis I wanted to use the TxDb.Hsapiens.UCSC.hg38.knownGene library to retrieve exon locations. However, when I run this code
library(TxDb.Hsapiens.UCSC.hg38.knownGene)
tx <- TxDb.Hsapiens.UCSC.hg38.knownGene
I get an error message that
No object 'TxDb.Hsapiens.UCSC.hg38.knownGene' was found.
What can I posibly do to solve this issue?
TxDb.Hsapiens.UCSC.hg38.knownGene
• 2.0k views
@james-w-macdonald-5106
Last seen 2 days ago
United States
You need to show your output from sessionInfo()
. Anyway, this works for me
> library(TxDb.Hsapiens.UCSC.hg38.knownGene)
> tx <- TxDb.Hsapiens.UCSC.hg38.knownGene
> tx
TxDb object:
# Db type: TxDb
# Supporting package: GenomicFeatures
# Data source: UCSC
# Genome: hg38
# Organism: Homo sapiens
# Taxonomy ID: 9606
# UCSC Table: knownGene
# UCSC Track: GENCODE v32
# Resource URL: http://genome.ucsc.edu/
# Type of Gene ID: Entrez Gene ID
# Full dataset: yes
# miRBase build ID: NA
# transcript_nrow: 247541
# exon_nrow: 687521
# cds_nrow: 302763
# Db created by: GenomicFeatures package from Bioconductor
# Creation time: 2019-10-21 20:50:00 +0000 (Mon, 21 Oct 2019)
# GenomicFeatures version at creation time: 1.37.4
# RSQLite version at creation time: 2.1.2
# DBSCHEMAVERSION: 1.2
> sessionInfo()
R version 4.0.0 (2020-04-24)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19041)
Matrix products: default
locale:
[1] LC_COLLATE=English_United States.1252
[2] LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C
[5] LC_TIME=English_United States.1252
attached base packages:
[1] stats4 parallel stats graphics grDevices utils datasets
[8] methods base
other attached packages:
[1] TxDb.Hsapiens.UCSC.hg38.knownGene_3.10.0
[2] GenomicFeatures_1.42.1
[3] AnnotationDbi_1.52.0
[4] Biobase_2.50.0
[5] GenomicRanges_1.42.0
[6] GenomeInfoDb_1.26.2
[7] IRanges_2.24.1
[8] S4Vectors_0.28.1
[9] BiocGenerics_0.36.0
loaded via a namespace (and not attached):
[1] SummarizedExperiment_1.20.0 progress_1.2.2
[3] tidyselect_1.1.0 purrr_0.3.4
[5] lattice_0.20-41 vctrs_0.3.6
[7] generics_0.1.0 BiocFileCache_1.14.0
[9] rtracklayer_1.50.0 blob_1.2.1
[11] XML_3.99-0.5 rlang_0.4.10
[13] pillar_1.4.7 glue_1.4.2
[15] DBI_1.1.0 BiocParallel_1.24.1
[17] rappdirs_0.3.1 bit64_4.0.5
[19] dbplyr_2.0.0 matrixStats_0.57.0
[21] GenomeInfoDbData_1.2.4 lifecycle_0.2.0
[23] MatrixGenerics_1.2.0 stringr_1.4.0
[25] zlibbioc_1.36.0 Biostrings_2.58.0
[27] memoise_1.1.0 biomaRt_2.46.0
[29] curl_4.3 Rcpp_1.0.5
[31] openssl_1.4.3 DelayedArray_0.16.0
[33] XVector_0.30.0 bit_4.0.4
[35] Rsamtools_2.6.0 hms_0.5.3
[37] askpass_1.1 digest_0.6.27
[39] stringi_1.5.3 dplyr_1.0.2
[41] grid_4.0.0 tools_4.0.0
[43] bitops_1.0-6 magrittr_2.0.1
[45] RCurl_1.98-1.2 RSQLite_2.2.1
[47] tibble_3.0.4 crayon_1.3.4
[49] pkgconfig_2.0.3 Matrix_1.2-18
[51] ellipsis_0.3.1 xml2_1.3.2
[53] prettyunits_1.1.1 assertthat_0.2.1
[55] httr_1.4.2 R6_2.5.0
[57] GenomicAlignments_1.26.0 compiler_4.0.0
If I were to guess, you haven't actually loaded the TxDb.Hsapiens.UCSC.hg38.knownGene
package.
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