hello ! I'm trying to use graphite to extrat direct interactions between molecules (so, without any intermediate molecules). I tried this with Reactome, but when i checked interactions obtained with graphite in Reactome, i see only a few direct interactions on PathwayBrowser, not all graphite results. Is there a way to get only the interactions i want on graphite ?

You can extract direct interactions from a pathway making use of the "type" attribute of each edge.

Taking a Reactome pathway as an example:

> library(graphite)
> library(dplyr)
> hsa <- pathways("hsapiens", "reactome")
> edges(hsa[["Apoptosis"]]) %>% filter(type=="Process(BiochemicalReaction)")
  src_type    src dest_type   dest direction                         type
1  UNIPROT P0CG47   UNIPROT Q13177  directed Process(BiochemicalReaction)
2  UNIPROT P0CG48   UNIPROT Q13177  directed Process(BiochemicalReaction)
3  UNIPROT P62979   UNIPROT Q13177  directed Process(BiochemicalReaction)
4  UNIPROT P62987   UNIPROT Q13177  directed Process(BiochemicalReaction)
5  UNIPROT Q13177   UNIPROT P0CG47  directed Process(BiochemicalReaction)
6  UNIPROT Q13177   UNIPROT P0CG48  directed Process(BiochemicalReaction)
7  UNIPROT Q13177   UNIPROT P62979  directed Process(BiochemicalReaction)
8  UNIPROT Q13177   UNIPROT P62987  directed Process(BiochemicalReaction)