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

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.

biostrings r

• 6,819 views • link

updated 4.8 years ago by Ram

• written 12.1 years ago by Aishwarya.Kulkarni •

Can you post the output of the following?

class(pwm)
class(seq)

• 0 views • link

updated 4.8 years ago by Ram

• written 12.1 years ago by Devon Ryan

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

• 0 views • link

updated 4.8 years ago by Ram

• written 12.1 years ago by Aishwarya.Kulkarni •

1 answer

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

• 0 views • link

updated 4.8 years ago by Ram

• written 12.1 years ago by Devon Ryan

Ok thank you so much.

• 0 views • link

written 12.1 years ago by Aishwarya.Kulkarni •

How do I convert a fasta sequence into DNAstring Object

• 0 views • link

written 12.1 years ago by Aishwarya.Kulkarni •

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