Hello i run this code from the manual but it appears this errorq Error in (function (classes, fdef, mtable) : unable to find an inherited method for function ‘matchPWM’ for signature ‘"standardGeneric" What did i do wrong?

 library(TFBSTools)
library(JASPAR2020)
library(Biostrings)
library(S4Vectors)

data(MA0003.2)
data(MA0004.1)
pwmList <- PWMatrixList(MA0003.2=toPWM(MA0003.2), MA0004.1=toPWM(MA0004.1),
                        use.names=TRUE)

SiteSetList <- searchSeq(pwmList, subject, seqname="seq1",
                        min.score="60%", strand="*")
subject <- DNAString("GAATTCTCTCTTGTTGTAGTCTCTTGACAAAATG")

Hi,

I think just the order is incorrect. As you can see, the second argument of function searchSeq is subject which is being assigned after the call to searchSeq in your code snippet. If you alter that, it should work.

library(TFBSTools)
library(JASPAR2020)
library(Biostrings)
library(S4Vectors)

data(MA0003.2)
data(MA0004.1)
pwmList <- PWMatrixList(MA0003.2=toPWM(MA0003.2), MA0004.1=toPWM(MA0004.1),
                        use.names=TRUE)

subject <- DNAString("GAATTCTCTCTTGTTGTAGTCTCTTGACAAAATG")
SiteSetList <- searchSeq(pwmList, subject, seqname="seq1",
                        min.score="60%", strand="*")

You can also check the same in TFBSTools' vignette here: https://bioconductor.org/packages/release/bioc/vignettes/TFBSTools/inst/doc/TFBSTools.html#searchseq

Hope it helps.