unable to find an inherited method for function matchPWM for signature "list"match

Question

[Aishwarya.Kulkarni]

Hi I am trying to use the function matchPWM which needs the pwm, sequence and the min score cutoff as the arguments,

I am giving the pwm and seq as follows:

> matchPWM(pwm, seq, min.score="60%")

and it is throwing me an error:

unable to find an inherited method for function matchPWM for signature '"list"'

Please let me know what could possibly be going wrong.

[Devon Ryan]

Can you post the output of the following?

class(pwm)
class(seq)

[Aishwarya.Kulkarni]

> class(pwm)
[1] "matrix"
> class(seq)
[1] "list"

Answer 1

[Devon Ryan]

seq should be a DNAString, not a list. Have a read through help(matchPWM).

[Aishwarya.Kulkarni]

Ok thank you so much.

[Aishwarya.Kulkarni]

How do I convert a fasta sequence into DNAstring Object