Biostrings: PWM with background probabilities
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Tim Smith ★ 1.1k
@tim-smith-1532
Last seen 7.9 years ago
Hi, I wanted to make a pwm with a frequency table. However, the background frequencies are given by a separate table. How can I incorporate these into the pwm? For example, my frequency table is:   1  2 3 4 5 6 7 8  9 10 A 3  3 1 2 1 5 4 2  3  6 G 2  1 2 5 4 3 3 3  1  5 C 8 10 7 6 7 6 7 8 10  0 T 2  1 5 2 3 1 1 2  1  4 and my background frequency/probability table is:         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 How do I go about making a PWM? many thanks! [[alternative HTML version deleted]]
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