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need help to generate an intersection matrix

2 messages · Li, Aiguo (NIH/NCI), Jim Lemon

Li, Aiguo (NIH/NCI)
# 
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
Jim Lemon
# 
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: