| countIntType_batch {netDx} | R Documentation |
Counts number of (+,+) and (+,-) interactions in a set of networks
countIntType_batch(inFiles, plusID, minusID, tmpDir = tempdir(), enrType = "binary", numCores = 1L)
inFiles |
(char) path to interaction networks to process |
plusID |
(char) IDs of + nodes |
minusID |
(char) IDs of - nodes |
tmpDir |
(char) path to dir where temporary files can be stored |
enrType |
(char) see getEnr.R |
numCores |
(integer) number of cores for parallel processing |
(matrix) two columns, one row per network
If enrType="binary", number of (+,+) and other interactions
Otherwise if enrType="corr" mean edge weight of (+,+) edges and
of other edges
d <- tempdir()
# write PSN
m1 <- matrix(c("P1","P1","P2","P2","P3","P4",1,1,1),byrow=FALSE,ncol=3)
write.table(m1,file=paste(d,"net1.txt",sep=getFileSep()),sep="\t",
col.names=FALSE,row.names=FALSE,quote=FALSE)
m2 <- matrix(c("P3","P4",1),nrow=1)
write.table(m2,file=paste(d,"net2.txt",sep=getFileSep()),sep="\t",
col.names=FALSE,row.names=FALSE,quote=FALSE)
countIntType_batch(paste(d,c("net1.txt","net2.txt"),sep=getFileSep()),
c("P1","P2","P3"),c("P4","P5"))