Convert homologous gene symbols in expression objects
Source:R/ConvertHomologs.R
ConvertHomologs.RdConvert feature names between species with GeneConvert and collapse duplicated target homologs by summing expression values. The Seurat method rebuilds the selected assay from the converted counts matrix and keeps cell metadata and spatial images when present.
Usage
ConvertHomologs(
object,
species_from,
species_to,
geneID_from_IDtype = "symbol",
geneID_to_IDtype = "symbol",
assay = NULL,
layer = "counts",
multi_mapping = c("first"),
keep_unmapped = FALSE,
collapse_fun = c("sum"),
Ensembl_version = NULL,
biomart = NULL,
mirror = NULL,
max_tries = 5,
verbose = TRUE
)
# S3 method for class 'Seurat'
ConvertHomologs(
object,
species_from,
species_to,
geneID_from_IDtype = "symbol",
geneID_to_IDtype = "symbol",
assay = NULL,
layer = "counts",
multi_mapping = c("first"),
keep_unmapped = FALSE,
collapse_fun = c("sum"),
Ensembl_version = NULL,
biomart = NULL,
mirror = NULL,
max_tries = 5,
verbose = TRUE
)
# S3 method for class 'matrix'
ConvertHomologs(
object,
species_from,
species_to,
geneID_from_IDtype = "symbol",
geneID_to_IDtype = "symbol",
assay = NULL,
layer = "counts",
multi_mapping = c("first"),
keep_unmapped = FALSE,
collapse_fun = c("sum"),
Ensembl_version = NULL,
biomart = NULL,
mirror = NULL,
max_tries = 5,
verbose = TRUE
)
# S3 method for class 'Matrix'
ConvertHomologs(
object,
species_from,
species_to,
geneID_from_IDtype = "symbol",
geneID_to_IDtype = "symbol",
assay = NULL,
layer = "counts",
multi_mapping = c("first"),
keep_unmapped = FALSE,
collapse_fun = c("sum"),
Ensembl_version = NULL,
biomart = NULL,
mirror = NULL,
max_tries = 5,
verbose = TRUE
)
# Default S3 method
ConvertHomologs(
object,
species_from,
species_to,
geneID_from_IDtype = "symbol",
geneID_to_IDtype = "symbol",
assay = NULL,
layer = "counts",
multi_mapping = c("first"),
keep_unmapped = FALSE,
collapse_fun = c("sum"),
Ensembl_version = NULL,
biomart = NULL,
mirror = NULL,
max_tries = 5,
verbose = TRUE
)Arguments
- object
A
Seuratobject or a gene-by-cell matrix.- species_from
Latin names for animals of the input geneID. e.g.
"Homo_sapiens","Mus_musculus".- species_to
Latin names for animals of the output geneID. e.g.
"Homo_sapiens","Mus_musculus".- geneID_from_IDtype
Gene ID type of the input
geneID. e.g."symbol","ensembl_id","entrez_id"- geneID_to_IDtype
Gene ID type(s) to convert to. e.g.
"symbol","ensembl_id","entrez_id".- assay
Assay to convert when
objectis aSeuratobject. IfNULL, the default assay is used.- layer
Assay layer used for conversion. Default
"counts".- multi_mapping
How to handle source genes mapped to multiple target homologs.
"first"keeps the first target homolog for each source gene.- keep_unmapped
Whether to keep unmapped source genes with their original names.
- collapse_fun
Function used to collapse duplicated target homologs. Currently only
"sum"is supported.- Ensembl_version
An integer specifying the Ensembl version. Default is
NULL. IfNULL, the latest version will be used.- biomart
The name of the BioMart database that you want to connect to. Possible options include
"ensembl","protists_mart","fungi_mart", and"plants_mart".- mirror
Specify an Ensembl mirror to connect to. The valid options here are
"www","uswest","useast","asia".- max_tries
The maximum number of attempts to connect with the BioMart service.
- verbose
Whether to print the message. Default is
TRUE.
Value
A converted object of the same high-level type as object. The
mapping table is stored in @tools$ConvertHomologs for Seurat objects and in
the "ConvertHomologs" attribute for matrix inputs.
See also
AnnotateFeatures, ConvertHomologs]
Examples
data(pancreas_sub)
pancreas_human <- ConvertHomologs(
pancreas_sub,
species_from = "Mus_musculus",
species_to = "Homo_sapiens"
)
#> ℹ [2026-07-02 08:32:32] Connect to the Ensembl archives...
#> ℹ [2026-07-02 08:32:35] Using the 116 version of ensembl database...
#> ℹ [2026-07-02 08:32:35] Downloading the ensembl database from https://jun2026.archive.ensembl.org...
#> Ensembl site unresponsive, trying www mirror
#> ℹ [2026-07-02 08:32:47] Searching the dataset mmusculus ...
#> ℹ [2026-07-02 08:32:48] Connecting to the dataset mmusculus_gene_ensembl ...
#> ℹ [2026-07-02 08:33:15] Converting the geneIDs...
#> ! [2026-07-02 08:33:56] <error/httr2_http_405>
#> ! Error in `httr2::req_perform()`:
#> ! ! HTTP 405 Method Not Allowed.
#> ! ---
#> ! Backtrace:
#> ! ▆
#> ! 1. ├─base::tryCatch(...)
#> ! 2. │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
#> ! 3. │ ├─base (local) tryCatchOne(...)
#> ! 4. │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
#> ! 5. │ └─base (local) tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
#> ! 6. │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
#> ! 7. │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
#> ! 8. ├─base::withCallingHandlers(...)
#> ! 9. ├─base::saveRDS(...)
#> ! 10. ├─base::do.call(...)
#> ! 11. ├─base (local) `<fn>`(...)
#> ! 12. └─global `<fn>`(...)
#> ! 13. └─pkgdown::build_site(...)
#> ! 14. └─pkgdown:::build_site_local(...)
#> ! 15. └─pkgdown::build_reference(...)
#> ! 16. ├─pkgdown:::unwrap_purrr_error(...)
#> ! 17. │ └─base::withCallingHandlers(...)
#> ! 18. └─purrr::map(...)
#> ! 19. └─purrr:::map_("list", .x, .f, ..., .progress = .progress)
#> ! 20. ├─purrr:::with_indexed_errors(...)
#> ! 21. │ └─base::withCallingHandlers(...)
#> ! 22. ├─purrr:::call_with_cleanup(...)
#> ! 23. └─pkgdown (local) .f(.x[[i]], ...)
#> ! 24. ├─base::withCallingHandlers(...)
#> ! 25. └─pkgdown:::data_reference_topic(...)
#> ! 26. └─pkgdown:::run_examples(...)
#> ! 27. └─pkgdown:::highlight_examples(code, topic, env = env)
#> ! 28. └─downlit::evaluate_and_highlight(...)
#> ! 29. └─evaluate::evaluate(code, child_env(env), new_device = TRUE, output_handler = output_handler)
#> ! 30. ├─base::withRestarts(...)
#> ! 31. │ └─base (local) withRestartList(expr, restarts)
#> ! 32. │ ├─base (local) withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
#> ! 33. │ │ └─base (local) doWithOneRestart(return(expr), restart)
#> ! 34. │ └─base (local) withRestartList(expr, restarts[-nr])
#> ! 35. │ └─base (local) withOneRestart(expr, restarts[[1L]])
#> ! 36. │ └─base (local) doWithOneRestart(return(expr), restart)
#> ! 37. ├─evaluate:::with_handlers(...)
#> ! 38. │ ├─base::eval(call)
#> ! 39. │ │ └─base::eval(call)
#> ! 40. │ └─base::withCallingHandlers(...)
#> ! 41. ├─base::withVisible(eval(expr, envir))
#> ! 42. └─base::eval(expr, envir)
#> ! 43. └─base::eval(expr, envir)
#> ! 44. └─scop::ConvertHomologs(...)
#> ! 45. └─scop:::ConvertHomologs.Seurat(...)
#> ! 46. └─scop:::ConvertHomologs.default(...)
#> ! 47. └─scop::GeneConvert(...)
#> ! 48. ├─thisutils::try_get(...)
#> ! 49. │ ├─base::tryCatch(...)
#> ! 50. │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
#> ! 51. │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
#> ! 52. │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
#> ! 53. │ └─base::eval.parent(substitute(expr))
#> ! 54. │ └─base::eval(expr, p)
#> ! 55. │ └─base::eval(expr, p)
#> ! 56. └─biomaRt::getBM(...)
#> ! 57. └─biomaRt:::.submitQueryXML(...)
#> ! 58. └─httr2::req_perform(req)
#> ! [2026-07-02 08:33:57] Get errors when retrieving information from the BioMart database
#> ! [2026-07-02 08:33:58] Retrying...
#> ! [2026-07-02 08:33:58] <error/httr2_http_405>
#> ! Error in `httr2::req_perform()`:
#> ! ! HTTP 405 Method Not Allowed.
#> ! ---
#> ! Backtrace:
#> ! ▆
#> ! 1. ├─base::tryCatch(...)
#> ! 2. │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
#> ! 3. │ ├─base (local) tryCatchOne(...)
#> ! 4. │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
#> ! 5. │ └─base (local) tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
#> ! 6. │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
#> ! 7. │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
#> ! 8. ├─base::withCallingHandlers(...)
#> ! 9. ├─base::saveRDS(...)
#> ! 10. ├─base::do.call(...)
#> ! 11. ├─base (local) `<fn>`(...)
#> ! 12. └─global `<fn>`(...)
#> ! 13. └─pkgdown::build_site(...)
#> ! 14. └─pkgdown:::build_site_local(...)
#> ! 15. └─pkgdown::build_reference(...)
#> ! 16. ├─pkgdown:::unwrap_purrr_error(...)
#> ! 17. │ └─base::withCallingHandlers(...)
#> ! 18. └─purrr::map(...)
#> ! 19. └─purrr:::map_("list", .x, .f, ..., .progress = .progress)
#> ! 20. ├─purrr:::with_indexed_errors(...)
#> ! 21. │ └─base::withCallingHandlers(...)
#> ! 22. ├─purrr:::call_with_cleanup(...)
#> ! 23. └─pkgdown (local) .f(.x[[i]], ...)
#> ! 24. ├─base::withCallingHandlers(...)
#> ! 25. └─pkgdown:::data_reference_topic(...)
#> ! 26. └─pkgdown:::run_examples(...)
#> ! 27. └─pkgdown:::highlight_examples(code, topic, env = env)
#> ! 28. └─downlit::evaluate_and_highlight(...)
#> ! 29. └─evaluate::evaluate(code, child_env(env), new_device = TRUE, output_handler = output_handler)
#> ! 30. ├─base::withRestarts(...)
#> ! 31. │ └─base (local) withRestartList(expr, restarts)
#> ! 32. │ ├─base (local) withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
#> ! 33. │ │ └─base (local) doWithOneRestart(return(expr), restart)
#> ! 34. │ └─base (local) withRestartList(expr, restarts[-nr])
#> ! 35. │ └─base (local) withOneRestart(expr, restarts[[1L]])
#> ! 36. │ └─base (local) doWithOneRestart(return(expr), restart)
#> ! 37. ├─evaluate:::with_handlers(...)
#> ! 38. │ ├─base::eval(call)
#> ! 39. │ │ └─base::eval(call)
#> ! 40. │ └─base::withCallingHandlers(...)
#> ! 41. ├─base::withVisible(eval(expr, envir))
#> ! 42. └─base::eval(expr, envir)
#> ! 43. └─base::eval(expr, envir)
#> ! 44. └─scop::ConvertHomologs(...)
#> ! 45. └─scop:::ConvertHomologs.Seurat(...)
#> ! 46. └─scop:::ConvertHomologs.default(...)
#> ! 47. └─scop::GeneConvert(...)
#> ! 48. ├─thisutils::try_get(...)
#> ! 49. │ ├─base::tryCatch(...)
#> ! 50. │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
#> ! 51. │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
#> ! 52. │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
#> ! 53. │ └─base::eval.parent(substitute(expr))
#> ! 54. │ └─base::eval(expr, p)
#> ! 55. │ └─base::eval(expr, p)
#> ! 56. └─biomaRt::getBM(...)
#> ! 57. └─biomaRt:::.submitQueryXML(...)
#> ! 58. └─httr2::req_perform(req)
#> ! [2026-07-02 08:33:58] Get errors when retrieving information from the BioMart database
#> ! [2026-07-02 08:33:59] Retrying...
#> ! [2026-07-02 08:34:00] <error/httr2_http_405>
#> ! Error in `httr2::req_perform()`:
#> ! ! HTTP 405 Method Not Allowed.
#> ! ---
#> ! Backtrace:
#> ! ▆
#> ! 1. ├─base::tryCatch(...)
#> ! 2. │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
#> ! 3. │ ├─base (local) tryCatchOne(...)
#> ! 4. │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
#> ! 5. │ └─base (local) tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
#> ! 6. │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
#> ! 7. │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
#> ! 8. ├─base::withCallingHandlers(...)
#> ! 9. ├─base::saveRDS(...)
#> ! 10. ├─base::do.call(...)
#> ! 11. ├─base (local) `<fn>`(...)
#> ! 12. └─global `<fn>`(...)
#> ! 13. └─pkgdown::build_site(...)
#> ! 14. └─pkgdown:::build_site_local(...)
#> ! 15. └─pkgdown::build_reference(...)
#> ! 16. ├─pkgdown:::unwrap_purrr_error(...)
#> ! 17. │ └─base::withCallingHandlers(...)
#> ! 18. └─purrr::map(...)
#> ! 19. └─purrr:::map_("list", .x, .f, ..., .progress = .progress)
#> ! 20. ├─purrr:::with_indexed_errors(...)
#> ! 21. │ └─base::withCallingHandlers(...)
#> ! 22. ├─purrr:::call_with_cleanup(...)
#> ! 23. └─pkgdown (local) .f(.x[[i]], ...)
#> ! 24. ├─base::withCallingHandlers(...)
#> ! 25. └─pkgdown:::data_reference_topic(...)
#> ! 26. └─pkgdown:::run_examples(...)
#> ! 27. └─pkgdown:::highlight_examples(code, topic, env = env)
#> ! 28. └─downlit::evaluate_and_highlight(...)
#> ! 29. └─evaluate::evaluate(code, child_env(env), new_device = TRUE, output_handler = output_handler)
#> ! 30. ├─base::withRestarts(...)
#> ! 31. │ └─base (local) withRestartList(expr, restarts)
#> ! 32. │ ├─base (local) withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
#> ! 33. │ │ └─base (local) doWithOneRestart(return(expr), restart)
#> ! 34. │ └─base (local) withRestartList(expr, restarts[-nr])
#> ! 35. │ └─base (local) withOneRestart(expr, restarts[[1L]])
#> ! 36. │ └─base (local) doWithOneRestart(return(expr), restart)
#> ! 37. ├─evaluate:::with_handlers(...)
#> ! 38. │ ├─base::eval(call)
#> ! 39. │ │ └─base::eval(call)
#> ! 40. │ └─base::withCallingHandlers(...)
#> ! 41. ├─base::withVisible(eval(expr, envir))
#> ! 42. └─base::eval(expr, envir)
#> ! 43. └─base::eval(expr, envir)
#> ! 44. └─scop::ConvertHomologs(...)
#> ! 45. └─scop:::ConvertHomologs.Seurat(...)
#> ! 46. └─scop:::ConvertHomologs.default(...)
#> ! 47. └─scop::GeneConvert(...)
#> ! 48. ├─thisutils::try_get(...)
#> ! 49. │ ├─base::tryCatch(...)
#> ! 50. │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
#> ! 51. │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
#> ! 52. │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
#> ! 53. │ └─base::eval.parent(substitute(expr))
#> ! 54. │ └─base::eval(expr, p)
#> ! 55. │ └─base::eval(expr, p)
#> ! 56. └─biomaRt::getBM(...)
#> ! 57. └─biomaRt:::.submitQueryXML(...)
#> ! 58. └─httr2::req_perform(req)
#> ! [2026-07-02 08:34:00] Get errors when retrieving information from the BioMart database
#> ! [2026-07-02 08:34:01] Retrying...
#> ! [2026-07-02 08:34:02] <error/httr2_http_405>
#> ! Error in `httr2::req_perform()`:
#> ! ! HTTP 405 Method Not Allowed.
#> ! ---
#> ! Backtrace:
#> ! ▆
#> ! 1. ├─base::tryCatch(...)
#> ! 2. │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
#> ! 3. │ ├─base (local) tryCatchOne(...)
#> ! 4. │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
#> ! 5. │ └─base (local) tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
#> ! 6. │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
#> ! 7. │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
#> ! 8. ├─base::withCallingHandlers(...)
#> ! 9. ├─base::saveRDS(...)
#> ! 10. ├─base::do.call(...)
#> ! 11. ├─base (local) `<fn>`(...)
#> ! 12. └─global `<fn>`(...)
#> ! 13. └─pkgdown::build_site(...)
#> ! 14. └─pkgdown:::build_site_local(...)
#> ! 15. └─pkgdown::build_reference(...)
#> ! 16. ├─pkgdown:::unwrap_purrr_error(...)
#> ! 17. │ └─base::withCallingHandlers(...)
#> ! 18. └─purrr::map(...)
#> ! 19. └─purrr:::map_("list", .x, .f, ..., .progress = .progress)
#> ! 20. ├─purrr:::with_indexed_errors(...)
#> ! 21. │ └─base::withCallingHandlers(...)
#> ! 22. ├─purrr:::call_with_cleanup(...)
#> ! 23. └─pkgdown (local) .f(.x[[i]], ...)
#> ! 24. ├─base::withCallingHandlers(...)
#> ! 25. └─pkgdown:::data_reference_topic(...)
#> ! 26. └─pkgdown:::run_examples(...)
#> ! 27. └─pkgdown:::highlight_examples(code, topic, env = env)
#> ! 28. └─downlit::evaluate_and_highlight(...)
#> ! 29. └─evaluate::evaluate(code, child_env(env), new_device = TRUE, output_handler = output_handler)
#> ! 30. ├─base::withRestarts(...)
#> ! 31. │ └─base (local) withRestartList(expr, restarts)
#> ! 32. │ ├─base (local) withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
#> ! 33. │ │ └─base (local) doWithOneRestart(return(expr), restart)
#> ! 34. │ └─base (local) withRestartList(expr, restarts[-nr])
#> ! 35. │ └─base (local) withOneRestart(expr, restarts[[1L]])
#> ! 36. │ └─base (local) doWithOneRestart(return(expr), restart)
#> ! 37. ├─evaluate:::with_handlers(...)
#> ! 38. │ ├─base::eval(call)
#> ! 39. │ │ └─base::eval(call)
#> ! 40. │ └─base::withCallingHandlers(...)
#> ! 41. ├─base::withVisible(eval(expr, envir))
#> ! 42. └─base::eval(expr, envir)
#> ! 43. └─base::eval(expr, envir)
#> ! 44. └─scop::ConvertHomologs(...)
#> ! 45. └─scop:::ConvertHomologs.Seurat(...)
#> ! 46. └─scop:::ConvertHomologs.default(...)
#> ! 47. └─scop::GeneConvert(...)
#> ! 48. ├─thisutils::try_get(...)
#> ! 49. │ ├─base::tryCatch(...)
#> ! 50. │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
#> ! 51. │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
#> ! 52. │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
#> ! 53. │ └─base::eval.parent(substitute(expr))
#> ! 54. │ └─base::eval(expr, p)
#> ! 55. │ └─base::eval(expr, p)
#> ! 56. └─biomaRt::getBM(...)
#> ! 57. └─biomaRt:::.submitQueryXML(...)
#> ! 58. └─httr2::req_perform(req)
#> ! [2026-07-02 08:34:02] Get errors when retrieving information from the BioMart database
#> ! [2026-07-02 08:34:03] Retrying...
#> ! [2026-07-02 08:34:04] <error/httr2_http_405>
#> ! Error in `httr2::req_perform()`:
#> ! ! HTTP 405 Method Not Allowed.
#> ! ---
#> ! Backtrace:
#> ! ▆
#> ! 1. ├─base::tryCatch(...)
#> ! 2. │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
#> ! 3. │ ├─base (local) tryCatchOne(...)
#> ! 4. │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
#> ! 5. │ └─base (local) tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
#> ! 6. │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
#> ! 7. │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
#> ! 8. ├─base::withCallingHandlers(...)
#> ! 9. ├─base::saveRDS(...)
#> ! 10. ├─base::do.call(...)
#> ! 11. ├─base (local) `<fn>`(...)
#> ! 12. └─global `<fn>`(...)
#> ! 13. └─pkgdown::build_site(...)
#> ! 14. └─pkgdown:::build_site_local(...)
#> ! 15. └─pkgdown::build_reference(...)
#> ! 16. ├─pkgdown:::unwrap_purrr_error(...)
#> ! 17. │ └─base::withCallingHandlers(...)
#> ! 18. └─purrr::map(...)
#> ! 19. └─purrr:::map_("list", .x, .f, ..., .progress = .progress)
#> ! 20. ├─purrr:::with_indexed_errors(...)
#> ! 21. │ └─base::withCallingHandlers(...)
#> ! 22. ├─purrr:::call_with_cleanup(...)
#> ! 23. └─pkgdown (local) .f(.x[[i]], ...)
#> ! 24. ├─base::withCallingHandlers(...)
#> ! 25. └─pkgdown:::data_reference_topic(...)
#> ! 26. └─pkgdown:::run_examples(...)
#> ! 27. └─pkgdown:::highlight_examples(code, topic, env = env)
#> ! 28. └─downlit::evaluate_and_highlight(...)
#> ! 29. └─evaluate::evaluate(code, child_env(env), new_device = TRUE, output_handler = output_handler)
#> ! 30. ├─base::withRestarts(...)
#> ! 31. │ └─base (local) withRestartList(expr, restarts)
#> ! 32. │ ├─base (local) withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
#> ! 33. │ │ └─base (local) doWithOneRestart(return(expr), restart)
#> ! 34. │ └─base (local) withRestartList(expr, restarts[-nr])
#> ! 35. │ └─base (local) withOneRestart(expr, restarts[[1L]])
#> ! 36. │ └─base (local) doWithOneRestart(return(expr), restart)
#> ! 37. ├─evaluate:::with_handlers(...)
#> ! 38. │ ├─base::eval(call)
#> ! 39. │ │ └─base::eval(call)
#> ! 40. │ └─base::withCallingHandlers(...)
#> ! 41. ├─base::withVisible(eval(expr, envir))
#> ! 42. └─base::eval(expr, envir)
#> ! 43. └─base::eval(expr, envir)
#> ! 44. └─scop::ConvertHomologs(...)
#> ! 45. └─scop:::ConvertHomologs.Seurat(...)
#> ! 46. └─scop:::ConvertHomologs.default(...)
#> ! 47. └─scop::GeneConvert(...)
#> ! 48. ├─thisutils::try_get(...)
#> ! 49. │ ├─base::tryCatch(...)
#> ! 50. │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
#> ! 51. │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
#> ! 52. │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
#> ! 53. │ └─base::eval.parent(substitute(expr))
#> ! 54. │ └─base::eval(expr, p)
#> ! 55. │ └─base::eval(expr, p)
#> ! 56. └─biomaRt::getBM(...)
#> ! 57. └─biomaRt:::.submitQueryXML(...)
#> ! 58. └─httr2::req_perform(req)
#> ! [2026-07-02 08:34:04] Get errors when retrieving information from the BioMart database
#> Error in try_get(expr = { biomaRt::getBM(mart = mart1, attributes = c(from_attr, "ensembl_gene_id"), filters = from_attr, values = list(geneID))}, max_tries = max_tries, error_message = "Get errors when retrieving information from the BioMart database"): <error/httr2_http_405> Error in `httr2::req_perform()`: ! HTTP 405
#> Method Not Allowed. --- Backtrace: ▆ 1. ├─base::tryCatch(...) 2. │ └─base
#> (local) tryCatchList(expr, classes, parentenv, handlers) 3. │ ├─base (local)
#> tryCatchOne(...) 4. │ │ └─base (local) doTryCatch(return(expr), name,
#> parentenv, handler) 5. │ └─base (local) tryCatchList(expr, names[-nh],
#> parentenv, handlers[-nh]) 6. │ └─base (local) tryCatchOne(expr, names,
#> parentenv, handlers[[1L]]) 7. │ └─base (local) doTryCatch(return(expr), name,
#> parentenv, handler) 8. ├─base::withCallingHandlers(...) 9.
#> ├─base::saveRDS(...) 10. ├─base::do.call(...) 11. ├─base (local) `<fn>`(...)
#> 12. └─global `<fn>`(...) 13. └─pkgdown::build_site(...) 14.
#> └─pkgdown:::build_site_local(...) 15. └─pkgdown::build_reference(...) 16.
#> ├─pkgdown:::unwrap_purrr_error(...) 17. │ └─base::withCallingHandlers(...)
#> 18. └─purrr::map(...) 19. └─purrr:::map_("list", .x, .f, ..., .progress =
#> .progress) 20. ├─purrr:::with_indexed_errors(...) 21. │
#> └─base::withCallingHandlers(...) 22. ├─purrr:::call_with_cleanup(...) 23.
#> └─pkgdown (local) .f(.x[[i]], ...) 24. ├─base::withCallingHandlers(...) 25.
#> └─pkgdown:::data_reference_topic(...) 26. └─pkgdown:::run_examples(...) 27.
#> └─pkgdown:::highlight_examples(code, topic, env = env) 28.
#> └─downlit::evaluate_and_highlight(...) 29. └─evaluate::evaluate(code,
#> child_env(env), new_device = TRUE, output_handler = output_handler) 30.
#> ├─base::withRestarts(...) 31. │ └─base (local) withRestartList(expr,
#> restarts) 32. │ ├─base (local) withOneRestart(withRestartList(expr,
#> restarts[-nr]), restarts[[nr]]) 33. │ │ └─base (local)
#> doWithOneRestart(return(expr), restart) 34. │ └─base (local)
#> withRestartList(expr, restarts[-nr]) 35. │ └─base (local) withOneRestart(expr,
#> restarts[[1L]]) 36. │ └─base (local) doWithOneRestart(return(expr), restart)
#> 37. ├─evaluate:::with_handlers(...) 38. │ ├─base::eval(call) 39. │ │
#> └─base::eval(call) 40. │ └─base::withCallingHandlers(...) 41.
#> ├─base::withVisible(eval(expr, envir)) 42. └─base::eval(expr, envir) 43.
#> └─base::eval(expr, envir) 44. └─scop::ConvertHomologs(...) 45.
#> └─scop:::ConvertHomologs.Seurat(...) 46.
#> └─scop:::ConvertHomologs.default(...) 47. └─scop::GeneConvert(...) 48.
#> ├─thisutils::try_get(...) 49. │ ├─base::tryCatch(...) 50. │ │ └─base
#> (local) tryCatchList(expr, classes, parentenv, handlers) 51. │ │ └─base
#> (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 52. │ │ └─base
#> (local) doTryCatch(return(expr), name, parentenv, handler) 53. │
#> └─base::eval.parent(substitute(expr)) 54. │ └─base::eval(expr, p) 55. │
#> └─base::eval(expr, p) 56. └─biomaRt::getBM(...) 57.
#> └─biomaRt:::.submitQueryXML(...) 58. └─httr2::req_perform(req)
rownames(pancreas_human)[1:5]
#> Error: object 'pancreas_human' not found