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
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