orthogene
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Published
20 hours ago •
neurogenomics
neurogenomics
convert_orthologs returning Error in names(object) <- nm : attempt to set an attribute on NULL
1. Bug description
When running conver_orthologs I get an error that I am trying to set attribute to NULL.
Console output
Preparing gene_df.
data.frame format detected.
Extracting genes from NOG.
4,174 genes extracted.
Converting rat ==> human orthologs using: gprofiler
Retrieving all organisms available in gprofiler.
Using stored `gprofiler_orgs`.
Mapping species name: rat
Common name mapping found for rat
1 organism identified from search: rnorvegicus
Retrieving all organisms available in gprofiler.
Using stored `gprofiler_orgs`.
Mapping species name: human
Common name mapping found for human
1 organism identified from search: hsapiens
Checking for genes without orthologs in human.
Extracting genes from input_gene.
4,285 genes extracted.
Extracting genes from ortholog_gene.
4,285 genes extracted.
Dropping 269 NAs of all kinds from ortholog_gene.
Checking for genes without 1:1 orthologs.
Dropping 45 genes that have multiple input_gene per ortholog_gene (many:1).
Dropping 11 genes that have multiple ortholog_gene per input_gene (1:many).
Filtering gene_df with gene_map
Adding input_gene col to gene_df.
Adding input_gene_standard col to gene_df.
Error in names(object) <- nm : attempt to set an attribute on NULL
--
Expected behaviour
A new column in my gene_df with the human orthologs matching the rat genes in $NOG.
2. Reproducible example
Code
orthologs=orthogene::convert_orthologs(gene_df = allrats_sigs,
gene_input = "NOG",
gene_output = "columns",
standardise_genes = "TRUE",
input_species = "rat",
output_species = "human")
Data
allrats_sigs$NOG [1] "ENSRNOG00000000047" "ENSRNOG00000000047" "ENSRNOG00000000047" "ENSRNOG00000000047" [5] "ENSRNOG00000000073" "ENSRNOG00000000073" "ENSRNOG00000000075" "ENSRNOG00000000075"...etc (If possible, upload a small sample of your data so that we can reproduce the bug on our end. If that's not possible, please at least include a screenshot of your data and other relevant details.)
3. Session info
(Add output of the R function utils::sessionInfo() below. This helps us assess version/OS conflicts which could be causing bugs.)
# Paste utils::sessionInfo() output
R version 4.3.1 (2023-06-16)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 22.04.2 LTS
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.10.0
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.10.0
locale:
[1] LC_CTYPE=en_AU.UTF-8 LC_NUMERIC=C LC_TIME=en_AU.UTF-8
[4] LC_COLLATE=en_AU.UTF-8 LC_MONETARY=en_AU.UTF-8 LC_MESSAGES=en_AU.UTF-8
[7] LC_PAPER=en_AU.UTF-8 LC_NAME=C LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=en_AU.UTF-8 LC_IDENTIFICATION=C
time zone: Etc/UTC
tzcode source: system (glibc)
attached base packages:
[1] grid stats4 stats graphics grDevices utils datasets methods base
other attached packages:
[1] org.Rn.eg.db_3.18.0 orthogene_1.8.0 ggpubr_0.6.0 ggplot2_3.4.2
[5] VennDiagram_1.7.3 futile.logger_1.4.3 ensembldb_2.26.0 AnnotationFilter_1.26.0
[9] GenomicFeatures_1.54.4 AnnotationDbi_1.64.1 Biobase_2.62.0 GenomicRanges_1.54.1
[13] GenomeInfoDb_1.38.8 IRanges_2.36.0 S4Vectors_0.40.2 BiocGenerics_0.48.1
[17] edgeR_4.0.16 limma_3.58.1
loaded via a namespace (and not attached):
[1] jsonlite_1.8.7 rstudioapi_0.15.0 magrittr_2.0.3
[4] fs_1.6.3 BiocIO_1.12.0 zlibbioc_1.48.2
[7] vctrs_0.6.3 memoise_2.0.1 Rsamtools_2.18.0
[10] RCurl_1.98-1.12 ggtree_3.10.1 rstatix_0.7.2
[13] htmltools_0.5.5 S4Arrays_1.2.1 progress_1.2.2
[16] lambda.r_1.2.4 curl_5.0.1 broom_1.0.5
[19] gridGraphics_0.5-1 SparseArray_1.2.4 htmlwidgets_1.6.2
[22] plotly_4.10.2 futile.options_1.0.1 cachem_1.0.8
[25] GenomicAlignments_1.38.2 lifecycle_1.0.3 pkgconfig_2.0.3
[28] Matrix_1.6-0 R6_2.5.1 fastmap_1.1.1
[31] GenomeInfoDbData_1.2.11 MatrixGenerics_1.14.0 aplot_0.2.2
[34] digest_0.6.33 colorspace_2.1-0 patchwork_1.2.0
[37] grr_0.9.5 DESeq2_1.42.1 RSQLite_2.3.6
[40] filelock_1.0.2 fansi_1.0.4 httr_1.4.6
[43] abind_1.4-5 compiler_4.3.1 remotes_2.4.2.1
[46] bit64_4.0.5 withr_2.5.0 backports_1.4.1
[49] BiocParallel_1.36.0 carData_3.0-5 DBI_1.2.2
[52] homologene_1.4.68.19.3.27 highr_0.10 ggsignif_0.6.4
[55] biomaRt_2.58.2 rappdirs_0.3.3 DelayedArray_0.28.0
[58] rjson_0.2.21 tools_4.3.1 ape_5.7-1
[61] glue_1.6.2 restfulr_0.0.15 nlme_3.1-162
[64] ggvenn_0.1.10 generics_0.1.3 gtable_0.3.3
[67] tidyr_1.3.0 data.table_1.14.8 hms_1.1.3
[70] xml2_1.3.5 car_3.1-2 utf8_1.2.3
[73] XVector_0.42.0 pillar_1.9.0 stringr_1.5.0
[76] yulab.utils_0.1.4 babelgene_22.9 dplyr_1.1.2
[79] treeio_1.26.0 BiocFileCache_2.10.2 lattice_0.21-8
[82] rtracklayer_1.62.0 bit_4.0.5 tidyselect_1.2.1
[85] locfit_1.5-9.9 Biostrings_2.70.3 knitr_1.43
[88] ProtGenerics_1.34.0 SummarizedExperiment_1.32.0 xfun_0.39
[91] statmod_1.5.0 matrixStats_1.2.0 stringi_1.7.12
[94] ggfun_0.1.4 lazyeval_0.2.2 yaml_2.3.7
[97] evaluate_0.21 codetools_0.2-19 tibble_3.2.1
[100] BiocManager_1.30.22 ggplotify_0.1.2 cli_3.6.1
[103] munsell_0.5.0 Rcpp_1.0.11 gprofiler2_0.2.3
[106] dbplyr_2.5.0 png_0.1-8 XML_3.99-0.14
[109] parallel_4.3.1 blob_1.2.4 prettyunits_1.1.1
[112] bitops_1.0-7 viridisLite_0.4.2 tidytree_0.4.6
[115] scales_1.2.1 purrr_1.0.1 crayon_1.5.2
[118] rlang_1.1.1 KEGGREST_1.42.0 formatR_1.14
