变换矩阵对列表

Question

我有这样的互信息矩阵：

 
X1053_at X117_at X121_at X1255_g_at X1294_at X1316_at X1320_at 
X1053_at 0 0.00040833 0.052000448 0.101470422 0.00040833 0.223143551 
X117_at  0.00040833 0 0.00040833 0.174561677 0.174561677 0.034204976 
X121_at  0.052000448 0.00040833 0 0.020410997 0.010309644 0.034204976 
X1255_g_at 0.101470422 0.174561677 0.020410997 0 0.020410997 0.174561677 
X1294_at 0.00040833 0.174561677 0.010309644 0.020410997 0 0.101470422 
X1316_at 0.223143551 0.034204976 0.034204976 0.174561677 0.101470422 0 
X1320_at 0.074226329 0.134540323 0.052000448 0.00368703 0.020410997 0.101470422 

的话，我想在R A基因列表标签deliminated矩阵如：

 
geneX geneY weight 
geneX geneY weight 
geneX geneY weight 
geneX geneY weight 
geneX geneY weight 
geneX geneY weight 

可能任何人都可以帮助我？ 其实我想通过Cytoscape中或gephi或...这个矩阵，然后进口到出口 感谢

Answer 1

下面的技巧可以帮助：

x <- as.matrix(read.table(textConnection("X1053_at X117_at X121_at X1255_g_at X1294_at X1316_at X1320_at 
X1053_at 0 0.00040833 0.052000448 0.101470422 0.00040833 0.223143551 
X117_at  0.00040833 0 0.00040833 0.174561677 0.174561677 0.034204976 
X121_at  0.052000448 0.00040833 0 0.020410997 0.010309644 0.034204976 
X1255_g_at 0.101470422 0.174561677 0.020410997 0 0.020410997 0.174561677 
X1294_at 0.00040833 0.174561677 0.010309644 0.020410997 0 0.101470422 
X1316_at 0.223143551 0.034204976 0.034204976 0.174561677 0.101470422 0 
X1320_at 0.074226329 0.134540323 0.052000448 0.00368703 0.020410997 0.101470422"), header=TRUE, row.names=1)) 

# not sure if this is correctly aligned as you have 7 column names for 6 columns 

as.data.frame(as.table(x)) 

结果：

  Var1  Var2  Freq 
1 X1053_at X117_at 0.00000000 
2  X117_at X117_at 0.00040833 
3  X121_at X117_at 0.05200045 
4 X1255_g_at X117_at 0.10147042 
5 X1294_at X117_at 0.00040833