Filling expr matrix for igraph
2
0
Entering edit mode
4.5 years ago
Spacebio ▴ 200

Hello,

I have a file containing 11300 genes, looking like this:

A   active      B
B   inactive    C
C   unknown     E
D   active      D
E   inactive    A
A   active      C
B   unknown     A
C   inactive    D
D   active      E
E   active      B

After I stack the genes, I get a matrix like this:

A   active
B   inactive
C   unknown
D   active
E   inactive
A   active
B   unknown
C   inactive
D   active
E   active
B   active
C   inactive
E   unknown
D   active
A   inactive
C   active
A   unknown
D   inactive
E   active
B   active

Then, I remove the duplicates and I get the following output:

A   active
B   inactive
C   unknown
D   active
E   inactive
B   unknown
C   inactive
E   active
B   active
E   unknown
A   inactive
C   active
A   unknown
D   inactive

After that, I would like to have a matrix like this:

    Active  Inactive    Unknown
A      1        1          1
B      1        1          1
C      1        1          1
D      1        1          0
E      1        1          1

I tried with the followong syntax:

m <- matrix(nrow = 1467, ncol = 4)
for(column in 1){
  m[, column] <- nodes$values
}

But with that I just construct the matrix without filling it. The 1467 is the total number of uniquegenes in my file. Can someone help me?

R igraph matrix • 1.0k views
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3
Entering edit mode
4.5 years ago
> bla
   V1       V4
1   A   active
2   B inactive
3   C  unknown
4   D   active
5   E inactive
6   B  unknown
7   C inactive
8   E   active
9   B   active
10  E  unknown
11  A inactive
12  C   active
13  A  unknown
14  D inactive
> table(bla)
   V4
V1  active inactive unknown
  A      1        1       1
  B      1        1       1
  C      1        1       1
  D      1        1       0
  E      1        1       1
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0
Entering edit mode

Thank you so much! I hate when the answer is so obvious that makes me feel dumb.

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1
Entering edit mode
4.5 years ago

with datamash:

$ datamash crosstab 1,2 --filler 0 < file.txt 
    active  inactive    unknown
A   1   1   1
B   1   1   1
C   1   1   1
D   1   1   0
E   1   1   1

input:

$ cat file.txt 
A   active
B   inactive
C   unknown
D   active
E   inactive
B   unknown
C   inactive
E   active
B   active
E   unknown
A   inactive
C   active
A   unknown
D   inactive
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