Dear all,

I'm having some trouble with setting the background and running the enrichment analysis using the STRINGdb package.

Specifically, when I set the background and run the enrichment analysis I get a data.frame with appropriate column names, but empty rows. Running the same script but without the steps setting the background gives an expected result for the enrichment analysis. Running the STRING analysis and plotting the network seems to give expected results after setting the background. Unfortunately I'm unable to supply the original data as it's too large to share, but input mass-spec proteomics data, formatted for input for the MSstats package.

Please excuse me if I forgot to include some details - this is my first time posting.

Many thanks, Sam

# Initialise STRING
string_db <- STRINGdb$new(version="11.5",
                          species=9606, 
                          score_threshold=700,
                          network_type="full",
                          input_directory="")

# Map whole dataset and use to set background
string_background <- string_db$map(as.data.frame(input), "ProteinName", removeUnmappedRows = TRUE) %>%
  .$STRING_id %>%
  unique()
string_db$set_background(string_background)

# New database using background
string_db <- STRINGdb$new(version="11.5",
                          species=9606, 
                          score_threshold=700,
                          network_type="full",
                          input_directory="",
                          backgroundV = string_background)

# Run enrichment
STRING_enrichment <- string_db$get_enrichment(STRING_dataset$STRING_id)

head(STRING_enrichment)

 [1] category                      term                          number_of_genes              
 [4] number_of_genes_in_background ncbiTaxonId                   inputGenes                   
 [7] preferredNames                p_value                       fdr                          
[10] description                  
<0 rows> (or 0-length row.names)

sessionInfo( )

R version 4.2.0 (2022-04-22 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19044)

Matrix products: default

locale:
[1] LC_COLLATE=English_New Zealand.utf8  LC_CTYPE=English_New Zealand.utf8    LC_MONETARY=English_New Zealand.utf8
[4] LC_NUMERIC=C                         LC_TIME=English_New Zealand.utf8    

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

other attached packages:
 [1] STRINGdb_2.10.1        org.Hs.eg.db_3.16.0    AnnotationDbi_1.60.2   IRanges_2.32.0         S4Vectors_0.36.2      
 [6] Biobase_2.58.0         BiocGenerics_0.44.0    clusterProfiler_4.6.2  ComplexHeatmap_2.14.0  EnhancedVolcano_1.16.0
[11] ggrepel_0.9.3          lubridate_1.9.2        forcats_1.0.0          stringr_1.5.0          dplyr_1.1.2           
[16] purrr_1.0.1            readr_2.1.4            tidyr_1.3.0            tibble_3.2.1           ggplot2_3.4.2         
[21] tidyverse_2.0.0        MSstats_4.6.0