error when running GSEA.Rmd

[Witold Wolski]

I am testing the new runscript run_all_wide.R. It fails with an error when running the function

runGSEA

on the first file.
"./data/2Grp_CF_a_vs_CF_b.txt"

> genesets <- GSEA$merged_data %>% 
+   distinct(geneSet, .keep_all = TRUE) %>% 
+   dplyr::mutate(set = paste0("<a href='",link,"'>",geneSet,"</a>")) %>% 
+   dplyr::select(set, description, ES, NES, pValue, FDR)
Error in .f(.x[[i]], ...) : object 'ES' not found
> GSEA$merged_data
# A tibble: 2,067 x 17
   userId.x geneSymbol geneName   entrezgene score gLink     geneSet  description      link      enrichmentScore normalizedEnric~ pValue     FDR  size plotPath  leadingEdgeNum userId.y                
   <chr>    <chr>      <chr>      <chr>      <dbl> <chr>     <chr>    <chr>            <chr>               <dbl>            <dbl>  <dbl>   <dbl> <int> <chr>              <int> <chr>                   
 1 A0FGR8   ESYT2      extended ~ 57488      2.30  https://~ GO:0010~ lipid localizat~ http://a~           0.534             1.77      0 0.0449     71 ./Projec~             25 A0FGR8;O00763;O60488;O7~
 2 A0MZ66   SHTN1      shootin 1  57698      0.746 https://~ GO:0007~ endoplasmic ret~ http://a~           0.716             2.00      0 0          33 ./Projec~             24 A0MZ66;O00429;O14657;O1~
 3 O00139   KIF2A      kinesin f~ 3796       1.73  https://~ GO:0006~ retrograde vesi~ http://a~           0.629             1.96      0 0.00311    50 ./Projec~             28 O00139;O15066;O43264;O7~

Ideed there is NO column ES or NES for the merged_data frame.
I commited a change which allows me to store the GSEA list which is passed to GSEA.Rmd.

Witek

[Lucas Kook]

WebGestaltR_0.3.0 is the version I used and it runs through and contains column names ES, NES. merged_data.tsv is written into the project directory by runGSEA(), check also the column names there. When I run it on the said file it contains the correct column names.

[Lucas Kook]

WebGestaltR_0.4.0 changed the column names.

[Witold Wolski]

fixed