Hi,

I was trying to use the keggLink function to find all genes associated with all reactions. However, it returned an error like this.

> keggLink("reaction","genes")
Error in .getUrl(url, .listParser, nameColumn = 1, valueColumn = 2) : 
  Bad Request (HTTP 400).

However, keggLink seems to work for enzymes and reactions and various other combinations.

Is there any way to fix this? If keggLink is not available, how else can I view the genes associated with each reaction (and hopefully make a data frame with that)?

Thanks

Below is my session info.

> BiocManager::valid()
[1] TRUE
> BiocManager::version()
[1] ‘3.10’
> BiocManager::valid()
[1] TRUE
> sessionInfo()
R version 3.6.1 (2019-07-05)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Sierra 10.12.6

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

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

other attached packages:
 [1] openxlsx_4.1.4      forcats_0.4.0       stringr_1.4.0       dplyr_0.8.3         purrr_0.3.3        
 [6] readr_1.3.1         tidyr_1.0.0         tibble_2.1.3        ggplot2_3.2.1       tidyverse_1.3.0    
[11] plyr_1.8.5          Biostrings_2.54.0   XVector_0.26.0      IRanges_2.20.1      S4Vectors_0.24.1   
[16] BiocVersion_3.10.1  BiocGenerics_0.32.0 KEGGREST_1.26.1     BiocManager_1.30.10

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.3       lubridate_1.7.4  lattice_0.20-38  png_0.1-7        assertthat_0.2.1 zeallot_0.1.0   
 [7] R6_2.4.1         cellranger_1.1.0 backports_1.1.5  reprex_0.3.0     httr_1.4.1       pillar_1.4.3    
[13] zlibbioc_1.32.0  rlang_0.4.2      lazyeval_0.2.2   curl_4.3         readxl_1.3.1     rstudioapi_0.10 
[19] munsell_0.5.0    broom_0.5.3      compiler_3.6.1   modelr_0.1.5     pkgconfig_2.0.3  tidyselect_0.2.5
[25] crayon_1.3.4     dbplyr_1.4.2     withr_2.1.2      grid_3.6.1       nlme_3.1-143     jsonlite_1.6    
[31] gtable_0.3.0     lifecycle_0.1.0  DBI_1.1.0        magrittr_1.5     scales_1.1.0     zip_2.0.4       
[37] cli_2.0.0        stringi_1.4.3    remotes_2.1.0    fs_1.3.1         xml2_1.2.2       generics_0.0.2  
[43] vctrs_0.2.1      tools_3.6.1      glue_1.3.1       hms_0.5.2        colorspace_1.4-1 rvest_0.3.5     
[49] haven_2.2.0

That combination is not available. Looking at the kegg website information for the reaction database http://rest.kegg.jp/info/reaction , it gives the possible linked databases.

eaction         KEGG Reaction Database
rn               Release 93.0+/12-31, Dec 19
                 Kanehisa Laboratories
                 11,336 entries

linked db        pathway
                 brite
                 module
                 ko
                 compound
                 glycan
                 rclass
                 enzyme

genes is not a possible linked db. In R this information is also available with

> keggInfo("reaction")

It seems like KEGGREST should be altered to give a more informative ERROR message.