iblacksand
commented
1 week ago Sorry for the delayed response.
This seems to be an error in the kMedoid clustering. if you add usekMedoid = FALSE as a parameter to the WebGestaltR function call, you should avoid this for now. I will work on a fix so this won't be necessary, but that should be a temporary solution.
Hi folks
I tried to use the R version of webgestalt. Unfortunately, it takes much more time to get things started than expected. I already tried everything in the browser and it worked fine. In R, however, I go from one error to the next. I think I am close to getting through completely. The interestGeneFile is the same I used online where it worked. Using the test interestingGenes.txt from webgestalt works perfectly as well. When I truncate my txt file and delete many of the gene symbols, I won't get an error but I wont get all the files in the result folder, i.e. the html file is missing and something else as well. Normally, I would want to use mmusculus, but for establishing, capitalized as gene symbols. In any case, also when i go for mmusculus and won't change anything in the gene list (only first letter capitalized), I get the same error (see below)
filt_LFC-1_p0.05.txt
Input: outputDirectory <- getwd() enrichResult <- WebGestaltR( enrichMethod = "ORA", organism = "hsapiens", enrichDatabase = "geneontology_Biological_Process", interestGeneFile = "filt_LFC-1_p0.05.txt", interestGeneType = "genesymbol", referenceSet = "genome", referenceGeneType = "genesymbol", isOutput = TRUE, outputDirectory = outputDirectory, projectName = NULL )
Output: Loading the functional categories... Loading the ID list... Loading the reference list... Summarizing the input ID list by GO Slim data... Performing the enrichment analysis... Error in writeLines(sapply(kRes$clusters, paste, collapse = "\t"), file.path(projectDir, : can only write character objects
sessionInfo() R version 4.4.1 (2024-06-14) Platform: x86_64-pc-linux-gnu Running under: Ubuntu 20.04.6 LTS
Matrix products: default BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0 LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0
locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=de_CH.UTF-8
[4] LC_COLLATE=en_US.UTF-8 LC_MONETARY=de_CH.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=de_CH.UTF-8 LC_NAME=C LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=de_CH.UTF-8 LC_IDENTIFICATION=C
time zone: Europe/Zurich tzcode source: system (glibc)
attached base packages: [1] stats graphics grDevices utils datasets methods base
other attached packages: [1] WebGestaltR_1.0.0 ggrepel_0.9.5 ggforce_0.4.2 viridis_0.6.5
[5] viridisLite_0.4.2 ggConvexHull_0.1.0 fgsea_1.30.0 edgeR_4.2.1
[9] limma_3.60.3 gghighcontrast_0.1.0 Rsubread_2.18.0 lubridate_1.9.3
[13] forcats_1.0.0 stringr_1.5.1 dplyr_1.1.4 purrr_1.0.2
[17] readr_2.1.5 tidyr_1.3.1 tibble_3.2.1 ggplot2_3.5.1
[21] tidyverse_2.0.0
loaded via a namespace (and not attached): [1] poolr_1.1-1 gridExtra_2.3 remotes_2.5.0 rlang_1.1.4
[5] magrittr_2.0.3 compiler_4.4.1 systemfonts_1.1.0 callr_3.7.6
[9] vctrs_0.6.5 profvis_0.3.8 pkgconfig_2.0.3 crayon_1.5.3
[13] fastmap_1.2.0 ellipsis_0.3.2 utf8_1.2.4 promises_1.3.0
[17] sessioninfo_1.2.2 tzdb_0.4.0 ps_1.7.7 bit_4.0.5
[21] xfun_0.46 cachem_1.1.0 jsonlite_1.8.8 later_1.3.2
[25] BiocParallel_1.38.0 tweenr_2.0.3 cluster_2.1.6 parallel_4.4.1
[29] R6_2.5.1 stringi_1.8.4 pkgload_1.4.0 iterators_1.0.14
[33] Rcpp_1.0.13 knitr_1.48 usethis_2.2.3 httpuv_1.6.15
[37] Matrix_1.7-0 timechange_0.3.0 tidyselect_1.2.1 rstudioapi_0.16.0
[41] doParallel_1.0.17 codetools_0.2-19 miniUI_0.1.1.1 curl_5.2.1
[45] processx_3.8.4 doRNG_1.8.6 pkgbuild_1.4.4 lattice_0.22-5
[49] shiny_1.8.1.1 withr_3.0.0 desc_1.4.3 urlchecker_1.0.1
[53] polyclip_1.10-6 pillar_1.9.0 rngtools_1.5.2 whisker_0.4.1
[57] foreach_1.5.2 generics_0.1.3 mathjaxr_1.6-0 vroom_1.6.5
[61] hms_1.1.3 munsell_0.5.1 scales_1.3.0 xtable_1.8-4
[65] apcluster_1.4.13 glue_1.7.0 tools_4.4.1 data.table_1.15.4
[69] locfit_1.5-9.10 fs_1.6.4 fastmatch_1.1-4 cowplot_1.1.3
[73] grid_4.4.1 devtools_2.4.5 colorspace_2.1-0 cli_3.6.3
[77] fansi_1.0.6 svglite_2.1.3 gtable_0.3.5 digest_0.6.36
[81] htmlwidgets_1.6.4 farver_2.1.2 memoise_2.0.1 htmltools_0.5.8.1
[85] lifecycle_1.0.4 httr_1.4.7 statmod_1.5.0 mime_0.12
[89] bit64_4.0.5 MASS_7.3-61