Hi,

I had a question about the package/function seqLogo. I had a set of sequences for which I want to plot the sequence Logo. However, the background frequencies are not 1/4. I have another matrix with the background frequencies. How can I incorporate these in the seqLogo too?

For example, my sequence frequency matrix is:

> freqmat
        1       2       3       4       5       6       7       8       9      10
A 0.20000 0.20000 0.06667 0.13333 0.06667 0.33333 0.26667 0.13333 0.20000 0.40000
G 0.13333 0.06667 0.13333 0.33333 0.26667 0.20000 0.20000 0.20000 0.06667 0.33333
C 0.53333 0.66667 0.46667 0.40000 0.46667 0.40000 0.46667 0.53333 0.66667 0.06667
T 0.13333 0.06667 0.33333 0.13333 0.20000 0.06667 0.06667 0.13333 0.06667 0.20000

and my background frequency matrix is:

> background_freq_mat
        1       2       3       4       5       6       7       8       9      10
A 0.22182 0.22320 0.22473 0.22234 0.22258 0.22234 0.22053 0.22102 0.22335 0.22099
G 0.27851 0.28159 0.27729 0.28225 0.28118 0.28125 0.28052 0.28357 0.27801 0.28031
C 0.28063 0.27739 0.28000 0.27885 0.27989 0.27691 0.28134 0.27925 0.27756 0.28011
T 0.21904 0.21782 0.21797 0.21655 0.21635 0.21950 0.21761 0.21615 0.22109 0.21859


I know that I can get the seqLogo using an assumed background frequency of 1/4 for each base by:

> seqLogo(freqmat)

But how do I incorporate the background frequencies too?

If I cannot do it with seqLogo, is there any other package available that might do the trick?


thanks!!
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