countIntType_batch: Counts number of (+,+) and (+,-) interactions in a set of...

In BaderLab/netDx: Network-based patient classifier

Description

Counts number of (+,+) and (+,-) interactions in a set of networks

Usage

countIntType_batch(
  inFiles,
  plusID,
  minusID,
  tmpDir = tempdir(),
  enrType = "binary",
  numCores = 1L
)

Arguments

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

Value

(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

Examples

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"))

BaderLab/netDx documentation built on Sept. 26, 2021, 9:13 a.m.