Entering edit mode
Hello everyone. I am trying to filter the protein-coding genes from a list using biomaRt, and I am getting an error. The weird thing is that I've used the same code chunk dozens of times without any problems. I'm using RStudio.
my code:
#Remove non conding
ensembl = useMart(biomart="ensembl", dataset="hsapiens_gene_ensembl")
IDs= c(Tissue_Spec_Cleaned$Gene)
proteincode <- getBM(attributes=c("ensembl_gene_id","gene_biotype"),
filters = c("ensembl_gene_id","biotype"),
values=list(IDs,"protein_coding"), mart=ensembl)
##
Error in `vctrs::vec_as_subscript()`:
! `...` must be empty.
x Problematic argument:
* call = call
Run `rlang::last_error()` to see where the error occurred.
rlang::last_error()
Error in make_ansi_style(x[["color"]]) :
Unknown style specification: br_magenta
I've already tried reloading R and reinstalling the package, but I have no idea where this error is coming from
my session:
> sessionInfo( )
R version 4.1.1 (2021-08-10)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19044)
Matrix products: default
locale:
[1] LC_COLLATE=Portuguese_Brazil.1252 LC_CTYPE=Portuguese_Brazil.1252
[3] LC_MONETARY=Portuguese_Brazil.1252 LC_NUMERIC=C
[5] LC_TIME=Portuguese_Brazil.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] readxl_1.3.1 biomaRt_2.48.3
loaded via a namespace (and not attached):
[1] Rcpp_1.0.7 lattice_0.20-44 prettyunits_1.1.1
[4] png_0.1-7 Rsamtools_2.8.0 Biostrings_2.60.2
[7] assertthat_0.2.1 digest_0.6.28 utf8_1.2.2
[10] BiocFileCache_2.0.0 cellranger_1.1.0 R6_2.5.1
[13] GenomeInfoDb_1.28.4 stats4_4.1.1 RSQLite_2.2.8
[16] httr_1.4.4 pillar_1.8.1 zlibbioc_1.38.0
[19] rlang_1.0.6 GenomicFeatures_1.44.2 progress_1.2.2
[22] lazyeval_0.2.2 curl_4.3.2 rstudioapi_0.13
[25] blob_1.2.2 S4Vectors_0.30.0 Matrix_1.5-2
[28] BiocParallel_1.26.2 stringr_1.4.1 ProtGenerics_1.24.0
[31] RCurl_1.98-1.4 bit_4.0.4 DelayedArray_0.18.0
[34] compiler_4.1.1 rtracklayer_1.52.1 pkgconfig_2.0.3
[37] BiocGenerics_0.38.0 tidyselect_1.2.0 KEGGREST_1.32.0
[40] SummarizedExperiment_1.22.0 tibble_3.1.4 GenomeInfoDbData_1.2.6
[43] IRanges_2.26.0 matrixStats_0.62.0 XML_3.99-0.7
[46] fansi_0.5.0 withr_2.5.0 crayon_1.5.2
[49] dplyr_1.0.7 dbplyr_2.1.1 rappdirs_0.3.3
[52] GenomicAlignments_1.28.0 bitops_1.0-7 grid_4.1.1
[55] lifecycle_1.0.3 DBI_1.1.1 AnnotationFilter_1.16.0
[58] magrittr_2.0.1 cli_3.0.1 stringi_1.7.5
[61] cachem_1.0.6 XVector_0.32.0 xml2_1.3.2
[64] filelock_1.0.2 ellipsis_0.3.2 vctrs_0.3.8
[67] generics_0.1.3 rjson_0.2.20 restfulr_0.0.13
[70] ensembldb_2.16.4 tools_4.1.1 bit64_4.0.5
[73] Biobase_2.52.0 glue_1.6.2 purrr_0.3.5
[76] hms_1.1.1 MatrixGenerics_1.4.3 parallel_4.1.1
[79] fastmap_1.1.0 yaml_2.3.5 AnnotationDbi_1.54.1
[82] GenomicRanges_1.44.0 memoise_2.0.1 BiocIO_1.2.0
Can you give an example of the values in
IDs
? I currently have no idea where and error from the vctrs package might be coming in, biomaRt doesn't use that package directly.Here are the IDs:
I also have no idea what is going on
EDIT: I just reinstalled vctrs and the code worked again. I don't know why, but vctrs was giving some conflict. Thanks
Great! I guess vectrs is used in one of the packages further down the stack. I'm glad it's working again.