countPatientsInNet: Count number of patients in a network

In BaderLab/netDx: Network-based patient classifier

Description

Count number of patients in a network

Usage

countPatientsInNet(netDir, fList, ids)

Arguments

netDir	(char) dir with network set
fList	(char) filenames of interaction networks to count in
ids	(char) patient IDs to look for

Details

This functionality is needed to count patient overlap when input data is in a form that results in highly missing data, rather than when the same measures are available for almost all patients. An example application is when patient networks are based on unique genomic events in each patients (e.g. CNVs or indels), rather than 'full-matrix' data (e.g. questionnaires or gene expression matrices). The former scenario requires an update in the list of eligible networks each time some type of patient subsetting is applied (e.g. label enrichment, or train/test split). A matrix with patient/network membership serves as a lookup table to prune networks as feature selection proceeds

Value

(matrix) Size P by N, where P is num patients and N is number of networks networks; a[i,j] =1 if patient i in network j, else 0

Examples

d <- tempdir()
pids <- paste("P",1:5,sep="")
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)
x <- countPatientsInNet(d,c("net1.txt","net2.txt"), pids)

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