Question

[jmaggiore]

Hi there, I just submitted this question on Paxtools github but figured I may get a response here as well –

What is the most efficient way if I have a list of around ~50 genes to output a data frame in r that contains only the controls-state-of interaction type but for all the ~50 genes? When I query using this code it just takes such a long time and is outputting way more than I need.

t1 <- graphPc(source = 50_genes, kind = "NEIGHBORHOOD", format = "SIF", verbose = TRUE, limit = 1)

[cannin]

Does this help?

> library(paxtoolsr)
> 
> sif <- downloadPc2("PathwayCommons12.All.hgnc.sif.gz", version="12")
> 
> genes <- c("A1BG", "AKT1", "A1CF", "CASP1", "CCL2")
> 
> filtered_sif <- filterSif(sif, ids=genes, interactionTypes="controls-state-change-of", idsBothParticipants=TRUE)
> filtered_sif
   PARTICIPANT_A         INTERACTION_TYPE PARTICIPANT_B
9           A1BG controls-state-change-of          AKT1
80          A1CF controls-state-change-of         CASP1
82          A1CF controls-state-change-of          CCL2