I'm trying to run protein-protein-interaction network analysis (PPI) out of R using the package STRINGdb. The package STRINGdb allows me to run some 'minimal' analysis, however I have some more specific needs : When I extract the interactions between given proteins, only the combined score is returned. In the context of some specific projects, however, I don't want not use the max of all types of (sub-)scores (like 'Textmining', 'Experiments', 'Co‑expression', etc), but to ignore some of them (like 'Textmining').
Does anyone have a hint how to access these specific scores (as it is possible when running an analysis site https://string-db.org/ by manually clicking in 'Settings' in the fiels 'active interaction sources:' ) ?
Many thanks in advance, Wolfgang Raffelsberger
Here a tiny exmaple / minimal code :
library(BiocManager) library("STRINGdb") string_db <- STRINGdb::STRINGdb$new(version="11.5", species=9606, score_threshold=200, input_directory="") # most recent data1 <- data.frame(Gene.name=c("tp53","atm","egfr"), STRING_id=c("9606.ENSP00000269305","9606.ENSP00000278616","9606.ENSP00000275493")) netwInt1 <- string_db$get_interactions(data1$STRING_id) head(netwInt1) # combined score only STRINGdb$help("get_interactions") # thus, the function operates with single argument only, no way to specify which scores I'd like to use ## My sessionInfo gives: sessionInfo( ) R version 4.1.1 (2021-08-10) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 19042) Matrix products: default locale:  LC_COLLATE=French_France.1252 LC_CTYPE=French_France.1252 LC_MONETARY=French_France.1252 LC_NUMERIC=C LC_TIME=French_France.1252 attached base packages:  parallel stats4 stats graphics grDevices utils datasets methods base other attached packages:  STRINGdb_2.4.1 BiocManager_1.30.16 EnsDb.Hsapiens.v79_2.99.0 ensembldb_2.16.4 AnnotationFilter_1.16.0 GenomicFeatures_1.44.1  GenomicRanges_1.44.0 GenomeInfoDb_1.28.1 org.Hs.eg.db_3.13.0 AnnotationDbi_1.54.1 IRanges_2.26.0 S4Vectors_0.30.0  Biobase_2.52.0 BiocGenerics_0.38.0