need help to generate an intersection matrix
Hi Ana,
Here is one way:
pathway1<-LETTERS[1:5]
pathway2<-c("A","C","F")
pathway3<-c("B","D","E")
intersect.mat<-matrix(0,nrow=3,ncol=3)
rownames(intersect.mat)<-paste("pathway",1:3,sep="")
colnames(intersect.mat)<-paste("pathway",1:3,sep="")
for(row in 1:3) {
for(col in 1:3)
intersect.mat[row,col]<-
sum(get(rownames(intersect.mat)[row])%in%
get(colnames(intersect.mat)[col]))
}
Jim
On Fri, Feb 3, 2017 at 6:54 AM, Li, Aiguo (NIH/NCI) [E]
<liai at mail.nih.gov> wrote:
Dear all,
I am new to r script and run into some difficulty with this simple task.
Here is my data: I need to find out the number of mutual intersected elements as shown below
data
pathway1 A B C D E
pathway2 A C F
pathway3 B D E
output
pathway1 pathway2 pathway3
pathway1 5 2 3
pathway2 2 3 0
pathway3 3 0 3
here is my script
tb = matrix(data =NA, nrow = 3, ncol = 3)
for(i in 1:3){
for(j in 1:3){
tb[i,j]=length(intersect(data[i,][!is.na(data[i,])], data[j,][!is.na(data[j,])]))
}
}
Ana
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