[R] For help in R coding

[Bansal, Vikas]

Dear all,

I am doing a project on variant calling using R.I am working on pileup file.There are 10 columns in my data frame and I want to count the number of A,C,G and T in each row for column 9.example of column 9 is given below-

            .a,g,,
            .t,t,,
            .,c,c,
            .,a,,,
            .,t,t,t
            .c,,g,^!.
            .g,ggg.^!,
            .$,,,,,.,
            a,g,,t,
            ,,,,,.,^!.
            ,$,,,,.,.

This is a bit confusing for me as these characters are in one column and how can we scan them for each row to print number of A,C,G and T for each row.
Most of the rows have      .         and      ,    and other symbols but we will ignore them.I just want to run a loop with a counter which will count the number of A,C,G and T for each row and will give output something like this-


A   C   G  T
1   0   1  0
0   0   0  2
0   2   0  0
1   0   0  0
0   0   0  3

This output is for first 5 rows from the example given above.

I am new to R can you please help me.I will be very thankful to you.



Thanking you,
Warm Regards
Vikas Bansal
Msc Bioinformatics
Kings College London