How to calculate Position weight matrix

[rehan1988]

Hi

I have generated the PFM -------> PPM--------->PWM

But I am confuse that how program calculate the each position weight from PFM. I under that formula which calculate the PWM
which is

Mk,j =log2 (Mk,j/bk

but according to this formula the weight matrix values does not matched could you please guide me how it calculates the positions
for exp PFM first column (extracted from PFM OF 4 by17)

A 6
C 3
G 9
T 6

---

2nd row
3/24= .125 for first position (PFM value)

bk= consider is .25 for each ACGT

So for the same position PWM value is 0 (log2 * .125/.25)

I used
d<- toPWM(D1, type="log2probratio")

the output is

A 0
C -.95 whereas its log2 is -1
G .56
T 0

Please guide thanks

[lvanacken]

Dear rehan1988

RDocumentation only provides documentation on the packages and does not maintain the packages it lists or provides support on questions related to the packages via it's open-source repository.

Would like to propose you to ask your question again in the respective repository of the R package you are working with.

Thanks
Lode