When I use decoupleR to obtain the progeny network data, the following error occurs：
> packageVersion("OmnipathR")
[1] ‘3.17.4’
> packageVersion("decoupleR")
[1] ‘2.9.7’
> traceback()
25: stop(msg)
24: value[[3L]](cond)
23: tryCatchOne(expr, names, parentenv, handlers[[1L]])
22: tryCatchList(expr, classes, parentenv, handlers)
21: tryCatch(OmnipathR::static_table(query = "annotations", resource = name,
organism = organism), error = function(e) {
msg <- sprintf(paste0("[decoupleR] Failed to download annotation resource `%s` ",
"from OmniPath. For more information, see the OmnipathR log."),
name)
OmnipathR::omnipath_msg("error", msg)
stop(msg)
})
20: value[[3L]](cond)
19: tryCatchOne(expr, names, parentenv, handlers[[1L]])
18: tryCatchList(expr, classes, parentenv, handlers)
17: tryCatch(OmnipathR::import_omnipath_annotations(resources = name,
..., wide = TRUE), error = function(e) {
tryCatch(OmnipathR::static_table(query = "annotations", resource = name,
organism = organism), error = function(e) {
msg <- sprintf(paste0("[decoupleR] Failed to download annotation resource `%s` ",
"from OmniPath. For more information, see the OmnipathR log."),
name)
OmnipathR::omnipath_msg("error", msg)
stop(msg)
})
})
16: tryCatch(OmnipathR::import_omnipath_annotations(resources = name,
..., wide = TRUE), error = function(e) {
tryCatch(OmnipathR::static_table(query = "annotations", resource = name,
organism = organism), error = function(e) {
msg <- sprintf(paste0("[decoupleR] Failed to download annotation resource `%s` ",
"from OmniPath. For more information, see the OmnipathR log."),
name)
OmnipathR::omnipath_msg("error", msg)
stop(msg)
})
}) %>% {
if (organism != 9606L)
OmnipathR::orthology_translate_column(., "uniprot", target_organism = organism,
replace = TRUE) %>% OmnipathR::translate_ids(., uniprot,
genesymbol, organism = organism)
else .
}
15: get_resource("PROGENy", organism = organism)
14: dplyr::distinct(., pathway, genesymbol, .keep_all = TRUE)
13: dplyr::mutate(., weight = as.double(weight), p_value = as.double(p_value))
12: dplyr::select(., genesymbol, p_value, pathway, weight)
11: dplyr::group_by(., pathway)
10: dplyr::group_split(.)
9: vctrs_vec_compat(.x, .purrr_user_env)
8: map_("list", .x, .f, ..., .progress = .progress)
7: purrr::map(., function(df) {
df %>% dplyr::arrange(p_value) %>% head(top)
})
6: list2(...)
5: dplyr::bind_rows(.)
4: dplyr::select(., pathway, genesymbol, weight, p_value)
3: rlang::set_names(., c("source", "target", "weight", "p_value"))
2: get_resource("PROGENy", organism = organism) %>% dplyr::distinct(pathway,
genesymbol, .keep_all = TRUE) %>% dplyr::mutate(weight = as.double(weight),
p_value = as.double(p_value)) %>% dplyr::select(genesymbol,
p_value, pathway, weight) %>% dplyr::group_by(pathway) %>%
dplyr::group_split() %>% purrr::map(function(df) {
df %>% dplyr::arrange(p_value) %>% head(top)
}) %>% dplyr::bind_rows() %>% dplyr::select(pathway, genesymbol,
weight, p_value) %>% rlang::set_names(c("source", "target",
"weight", "p_value"))
1: decoupleR::get_progeny(organism = "mouse", top = 500)
> sessionInfo()
R version 4.3.1 (2023-06-16 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19045)
Matrix products: default
locale:
[1] LC_COLLATE=Chinese (Simplified)_China.utf8 LC_CTYPE=Chinese (Simplified)_China.utf8
[3] LC_MONETARY=Chinese (Simplified)_China.utf8 LC_NUMERIC=C
[5] LC_TIME=Chinese (Simplified)_China.utf8
time zone: Asia/Shanghai
tzcode source: internal
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] RcppAnnoy_0.0.22 splines_4.3.1 later_1.4.3 cellranger_1.1.0 tibble_3.3.0
[6] R.oo_1.27.1 polyclip_1.10-7 XML_3.99-0.19 fastDummies_1.7.5 lifecycle_1.0.4
[11] httr2_1.2.1 tcltk_4.3.1 vroom_1.6.5 globals_0.18.0 lattice_0.22-7
[16] MASS_7.3-60.0.1 backports_1.5.0 magrittr_2.0.3 openxlsx_4.2.8 plotly_4.11.0
[21] rmarkdown_2.29 yaml_2.3.10 httpuv_1.6.16 Seurat_5.3.0 sctransform_0.4.2
[26] spam_2.11-1 zip_2.3.2 askpass_1.2.1 sessioninfo_1.2.3 sp_2.2-0
[31] spatstat.sparse_3.1-0 reticulate_1.43.0 cowplot_1.2.0 pbapply_1.7-4 DBI_1.2.3
[36] RColorBrewer_1.1-3 lubridate_1.9.4 abind_1.4-8 rvest_1.0.4 Rtsne_0.17
[41] purrr_1.1.0 R.utils_2.13.0 rappdirs_0.3.3 gdtools_0.4.2 ggrepel_0.9.6
[46] irlba_2.3.5.1 listenv_0.9.1 spatstat.utils_3.1-5 pheatmap_1.0.13 goftest_1.2-3
[51] RSpectra_0.16-2 spatstat.random_3.4-1 fitdistrplus_1.2-4 parallelly_1.45.1 codetools_0.2-20
[56] xml2_1.4.0 tidyselect_1.2.1 farver_2.1.2 matrixStats_1.5.0 spatstat.explore_3.5-2
[61] jsonlite_2.0.0 progressr_0.15.1 ggridges_0.5.6 survival_3.8-3 systemfonts_1.2.3
[66] progress_1.2.3 tools_4.3.1 ragg_1.4.0 ica_1.0-3 Rcpp_1.1.0
[71] glue_1.8.0 gridExtra_2.3 xfun_0.53 decoupleR_2.9.7 dplyr_1.1.4
[76] withr_3.0.2 fastmap_1.2.0 openssl_2.3.3 digest_0.6.37 timechange_0.3.0
[81] R6_2.6.1 mime_0.13 textshaping_1.0.1 scattermore_1.2 tensor_1.5.1
[86] spatstat.data_3.1-8 RSQLite_2.4.3 R.methodsS3_1.8.2 tidyr_1.3.1 generics_0.1.4
[91] fontLiberation_0.1.0 data.table_1.17.8 prettyunits_1.2.0 httr_1.4.7 htmlwidgets_1.6.4
[96] uwot_0.2.3 pkgconfig_2.0.3 gtable_0.3.6 blob_1.2.4 lmtest_0.9-40
[101] selectr_0.4-2 OmnipathR_3.17.4 htmltools_0.5.8.1 fontBitstreamVera_0.1.1 dotCall64_1.2
[106] rvg_0.3.5 SeuratObject_5.1.0 scales_1.4.0 png_0.1-8 spatstat.univar_3.1-4
[111] knitr_1.50 rstudioapi_0.17.1 tzdb_0.5.0 reshape2_1.4.4 uuid_1.2-1
[116] checkmate_2.3.3 nlme_3.1-168 curl_7.0.0 zoo_1.8-14 cachem_1.1.0
[121] flextable_0.9.9 stringr_1.5.1 KernSmooth_2.23-26 parallel_4.3.1 miniUI_0.1.2
[126] pillar_1.11.0 grid_4.3.1 logger_0.4.0 vctrs_0.6.5 RANN_2.6.2
[131] promises_1.3.3 xtable_1.8-4 cluster_2.1.8.1 evaluate_1.0.4 readr_2.1.5
[136] cli_3.6.5 compiler_4.3.1 rlang_1.1.6 crayon_1.5.3 future.apply_1.20.0
[141] plyr_1.8.9 fs_1.6.6 stringi_1.8.7 viridisLite_0.4.2 deldir_2.0-4
[146] BiocParallel_1.36.0 lazyeval_0.2.2 spatstat.geom_3.5-0 fontquiver_0.2.1 Matrix_1.6-5
[151] RcppHNSW_0.6.0 hms_1.1.3 patchwork_1.3.1 bit64_4.6.0-1 future_1.67.0
[156] ggplot2_3.5.2 jjAnno_0.0.3 devEMF_4.5-1 stargazer_5.2.3 shiny_1.11.1
[161] ROCR_1.0-11 igraph_2.1.4 broom_1.0.9 memoise_2.0.1 bit_4.6.0
[166] export_0.3.2 readxl_1.4.5 officer_0.6.10
When I use decoupleR to obtain the progeny network data, the following error occurs：
Traceback
SessionInfo