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

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 âmatchPWM for signature '"list"'

Please let me know what could possibly be going wrong.

R Biostrings • 5.1k views
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Can you post the output of the following?

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

 

> class(seq)
[1] "list"

 

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7.3 years ago

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

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Ok thank you so much.

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How do I convert a fasta sequence into DNAstring Object

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