I am really new with R - so my question might be simple:
I have to plot average dinucleotides ratio profile over genes in each position upstream and downstream the TSS.
something like that :plot
By given a bed file with all these coordinates.
For example: one plot for AA/TT ratio on each position 3 kb upstream the TSS.
I found the SeqPattern package that might be helpful.
But on it's basics it calculates the frequency of each dinucleotides, when I would like to calculate the ratio.
Is there is a simple way to do it?
Or maybe use another package?