How to create an edge list from a matrix in R?

Question

The relationship is expressed as a matrix x like this:

      A    B    C     D
A     0    2    1     1
B     2    0    1     0
C     1    1             


        

Answer 1

using melt in reshape2, and then delete the weight==0. if no need to print the weight. just delete it.

x
    sample1 sample2 sample3 sample4
feature1       0       2       1       1
feature2       2       0       1       0
feature3       1       1       0       1
feature4       1       0       1       0

melt(x)
   Var1    Var2 value
1  feature1 sample1     0
2  feature2 sample1     2
3  feature3 sample1     1
4  feature4 sample1     1
5  feature1 sample2     2