library(msigdbr)
all_gene_sets <- msigdbr(species = "Mus musculus")
head(all_gene_sets)
Error in parse(text = elt): <text>:1:5: simbolo inatteso
1: Use of
^
Traceback:
1. msigdbr(species = "Mus musculus")
2. orthologs(genes = genesets_subset$human_ensembl_gene, species = species) %>%
. select(-any_of(c("human_symbol", "human_entrez"))) %>% rename(human_ensembl_gene = .data$human_ensembl,
. gene_symbol = .data$symbol, entrez_gene = .data$entrez, ensembl_gene = .data$ensembl,
. ortholog_sources = .data$support, num_ortholog_sources = .data$support_n)
3. rename(., human_ensembl_gene = .data$human_ensembl, gene_symbol = .data$symbol,
. entrez_gene = .data$entrez, ensembl_gene = .data$ensembl,
. ortholog_sources = .data$support, num_ortholog_sources = .data$support_n)
4. rename.data.frame(., human_ensembl_gene = .data$human_ensembl,
. gene_symbol = .data$symbol, entrez_gene = .data$entrez, ensembl_gene = .data$ensembl,
. ortholog_sources = .data$support, num_ortholog_sources = .data$support_n)
5. tidyselect::eval_rename(expr(c(...)), .data)
6. rename_impl(data, names(data), as_quosure(expr, env), strict = strict,
. name_spec = name_spec, allow_predicates = allow_predicates,
. error_call = error_call)
7. eval_select_impl(x, names, {
. {
. sel
. }
. }, strict = strict, name_spec = name_spec, type = "rename", allow_predicates = allow_predicates,
. error_call = error_call)
8. with_subscript_errors(out <- vars_select_eval(vars, expr, strict = strict,
. data = x, name_spec = name_spec, uniquely_named = uniquely_named,
. allow_rename = allow_rename, allow_empty = allow_empty, allow_predicates = allow_predicates,
. type = type, error_call = error_call), type = type)
9. try_fetch(expr, vctrs_error_subscript = function(cnd) {
. cnd$subscript_action <- subscript_action(type)
. cnd$subscript_elt <- "column"
. cnd_signal(cnd)
. })
10. withCallingHandlers(expr, vctrs_error_subscript = function(cnd) {
. {
. .__handler_frame__. <- TRUE
. .__setup_frame__. <- frame
. }
. out <- handlers[[1L]](cnd)
. if (!inherits(out, "rlang_zap"))
. throw(out)
. })
11. vars_select_eval(vars, expr, strict = strict, data = x, name_spec = name_spec,
. uniquely_named = uniquely_named, allow_rename = allow_rename,
. allow_empty = allow_empty, allow_predicates = allow_predicates,
. type = type, error_call = error_call)
12. walk_data_tree(expr, data_mask, context_mask)
13. eval_c(expr, data_mask, context_mask)
14. reduce_sels(node, data_mask, context_mask, init = init)
15. walk_data_tree(new, data_mask, context_mask)
16. expr_kind(expr, context_mask, error_call)
17. call_kind(expr, context_mask, error_call)
18. lifecycle::deprecate_soft("1.2.0", what, details = cli::format_inline("Please use {.code {str}} instead of `.data${var}`"),
. user_env = env)
19. signal_stage("deprecated", what)
20. spec(what, env = env)
21. spec_what(spec, "spec", signaller)
22. parse_expr(what)
23. parse_exprs(x)
24. chr_parse_exprs(x)
25. map(x, function(elt) as.list(parse(text = elt)))
26. lapply(.x, .f, ...)
27. FUN(X[[i]], ...)
28. as.list(parse(text = elt))
29. parse(text = elt)
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