multiGSEA package in R not appropriately assigning metabolites to pathways?
Entering edit mode
Thomas • 0
Last seen 7 months ago
United States

I've been trying to use the multiGSEA package to generate a combined p-value for pathways merging transcriptomics and metabolomics. Following the vignette, all worked fine until this part:

Even in the vignette, you can see the problem I've encountered- it seems to me that the metabolite mapping is not appropriately assigning metabolites to their respective pathways (the vignette shows NAs for metabolites instead of metabolites within each pathway).

Is there a bad link or should the syntax be different?

I tried mapping the HMDB inputs to KEGG and had some limited success - I could then at least view KEGG pathways, but the other 7 still didn't map correctly.

Any help is greatly appreciated!

include your problematic code here with any corresponding output

databases <- c( "kegg", "reactome")
layers <- names( omics_data)

pathways <- getMultiOmicsFeatures( dbs = databases, layer = layers,
                                   returnTranscriptome = "SYMBOL",
                                   returnProteome = "SYMBOL",
                                   returnMetabolome = "HMDB",
                                   useLocal = FALSE)
pathways_short <- lapply( names( pathways), function( name){
                          head( pathways[[name]], 2)
names( pathways_short) <- names( pathways)

$metabolome$`(KEGG) Glycolysis / Gluconeogenesis`
 [1] "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA"
[19] "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA"

$metabolome$`(KEGG) Citrate cycle (TCA cycle)`
 [1] "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA"
[19] "NA" "NA"

please also include the results of running the following in an R session

sessionInfo( ) -- note: I've also loaded this using the development version and found the same issue: R version 4.1.3 (2022-03-10) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 19042)

Matrix products: default

locale: [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C
[5] LC_TIME=English_United States.1252

attached base packages: [1] stats4 stats graphics grDevices utils datasets methods base

other attached packages: [1] beepr_1.3 AnnotationDbi_1.56.2
[4] IRanges_2.28.0 S4Vectors_0.32.4 Biobase_2.54.0
[7] AnnotationHub_3.2.2 BiocFileCache_2.2.1 dbplyr_2.3.0
[10] BiocGenerics_0.40.0 metaboliteIDmapping_1.0.0 magrittr_2.0.3
[13] multiGSEA_1.7.1 BiocParallel_1.28.3

loaded via a namespace (and not attached): [1] bitops_1.0-7 bit64_4.0.5 filelock_1.0.2
[4] httr_1.4.4 GenomeInfoDb_1.30.1 numDeriv_2016.8-1.1
[7] tools_4.1.3 backports_1.4.1 utf8_1.2.2
[10] R6_2.5.1 DBI_1.1.3 colorspace_2.0-3
[13] sn_2.1.0 withr_2.5.0 tidyselect_1.2.0
[16] graphite_1.40.0 gridExtra_2.3 mnormt_2.1.1
[19] bit_4.0.5 curl_5.0.0 compiler_4.1.3
[22] graph_1.72.0 cli_3.6.0 TFisher_0.2.0
[25] sandwich_3.0-2 scales_1.2.1 checkmate_2.1.0
[28] mvtnorm_1.1-3 rappdirs_0.3.3 stringr_1.5.0
[31] digest_0.6.31 rmarkdown_2.19 XVector_0.34.0
[34] htmltools_0.5.4 pkgconfig_2.0.3 plotrix_3.8-2
[37] fastmap_1.1.0 rlang_1.0.6 rstudioapi_0.14
[40] RSQLite_2.2.20 shiny_1.7.4 generics_0.1.3
[43] zoo_1.8-11 dplyr_1.0.10 RCurl_1.98-1.9
[46] GenomeInfoDbData_1.2.7 Matrix_1.5-3 Rcpp_1.0.9
[49] munsell_0.5.0 fansi_1.0.3 lifecycle_1.0.3
[52] stringi_1.7.6 multcomp_1.4-20 yaml_2.3.6
[55] mathjaxr_1.6-0 MASS_7.3-58.1 zlibbioc_1.40.0
[58] grid_4.1.3 blob_1.2.3 promises_1.2.0.1
[61] parallel_4.1.3 crayon_1.5.2 lattice_0.20-45
[64] Biostrings_2.62.0 splines_4.1.3 multtest_2.50.0
[67] KEGGREST_1.34.0 qqconf_1.3.1 knitr_1.41
[70] pillar_1.8.1 fgsea_1.20.0 codetools_0.2-18
[73] fastmatch_1.1-3 mutoss_0.1-12 glue_1.6.2
[76] BiocVersion_3.14.0 evaluate_0.19 metap_1.8
[79] data.table_1.14.6 BiocManager_1.30.19 httpuv_1.6.8
[82] png_0.1-8 vctrs_0.5.1 Rdpack_2.4
[85] purrr_1.0.1 gtable_0.3.1 assertthat_0.2.1
[88] cachem_1.0.6 ggplot2_3.4.0 xfun_0.36
[91] mime_0.12 rbibutils_2.2.13 xtable_1.8-4
[94] later_1.3.0 survival_3.5-0 audio_0.1-10
[97] snow_0.4-4 tibble_3.1.8 memoise_2.0.1
[100] ellipsis_0.3.2 TH.data_1.1-1 interactiveDisplayBase_1.32.0 ```

metaboliteIDmapping AnnotationHub multiGSEA • 455 views
Entering edit mode
Thomas • 0
Last seen 7 months ago
United States

I reached out to the multiGSEA package developer, and he responded that there was a problem where the tibble from metaboliteIDmapping was not imported into the Namespace of the multiGSEA package in the current version. He has pushed a bug fix in the devel and release branch of Bioconductor, so if anyone else comes across a similar issue, use the devel version or wait for the future update.


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