With paxtoolsr the heap size can also be increased; see below

# Change heap size when using paxtoolsr 
options(java.parameters = "-Xmx4g")

gzFile <- "PathwayCommons.8.reactome.BIOPAX.owl.gz"
owlFile <- "PathwayCommons.8.reactome.BIOPAX.owl"
untar(gzFile, exdir=".")

out1 <- "out1.out"
out2 <- "out2.out"
t1 <- getNeighbors(owlFile, out1, "")

But what I anticipate what you want to do is not completely straight-forward with getNeighbors(). You cannot simply pass gene IDs to getNeighbors with either in paxtools (or paxtoolsr that calls paxtools getNeighbors). You need to pass in URIs 

NOTE: Equivalent paxtools command: java -Xmx4g -jar paxtools-4.3.1.jar getNeighbors PathwayCommons.8.reactome.BIOPAX.owl cmd.out

You'll end up with a BioPAX file that can be converted to a SIF

t2 <- toSif(t1, out2)

In my understanding of getNeighbors this will return all the genes and small molecules that interact with GNG2 **PLUS** all the genes those entities interact with 

I wrote the filterSif function does not use the URIs that I use pretty often for research projects: 

sif <- downloadPc2("PathwayCommons.8.reactome.BINARY_SIF.hgnc.txt.sif.gz", version="8")
filteredSif <- filterSif(sif, ids="SDC1", interactionTypes="controls-state-change-of")

This allows you to use gene symbols and ignore interaction types you might not want. But you need the development version from GitHub ( if you want this functionality:

# Install 
if(!require(devtools)) { install.packages("devtools") }

gp <- graphPc(kind="NEIGHBORHOOD", datasource="reactome", format="BINARY_SIF", source="SDC1")
cannin/paxtoolsr documentation built on Jan. 13, 2018, 4:53 p.m.