Error in TFBSTools at SitesetList
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@ba287559
Last seen 9 weeks ago
Greece

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")
error TFBSTools R • 150 views
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@sarveshnikumbh-13961
Last seen 1 day ago
United Kingdom

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.

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Thank you very much. It was very simple but i was stuck. It helps me a lot!

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