replace value of each rows with value of column?

Question

[star]

 I have a table like as below. I like to replace each sample value base on comparing with third first columns and code each value with(0,1,2,3). For example, if sample value in each row = REF_REF -> 1 ; if sample value in each row = REF_ALT -> 2 ; if sample value in each row = ALT_ALT -> 3 and for 0/0 -> 0.

    REF_REF   REF_ALT   ALT_ALT       sample1       sample2     sample3

     A/A         A/G     G/G             0/0          A/G          G/G

    T/T          T/C     C/C             T/T          T/C          T/C

    C/C          C/G    G/G              0/0          C/G          C/G

I like to make a table like as:

    REF_REF   REF_ALT   ALT_ALT       sample1       sample2     sample3

    A/A         A/G       G/G           0               2           3

    T/T         T/C       C/C           1               2           2

    C/C        C/G       G/G            0               2           2

[Jimbou]

How many columns do you have? A correlation analysis between single values does not work.

[star]

Actually I have two columns but, I can get mean from those and make 1 column?

[Jimbou]

No, as already said a correlation analysis between single values does not work. I suggest that you read tutorials about the principles of correlation analysis (pearson, spearman) or learning by doing in R.

[Michael]

Did I miss something? Why do you refer to correlation analysis? Has the question been changed?

[Giovanni M Dall'Olio]

Yes, the OP changed the original question completely.

[Giovanni M Dall'Olio]

The way to do it is cor(t(mydataframe)). However as Jimbou correctly says, it doesn't make any sense for only one or two values.