PWMEnruch: Error in getPromoters(organism)
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prp291 • 0
@prp291-9622
Last seen 6.8 years ago

I am working with unsupported genome. Although similar question was asked before ( getBackgroundFrequencies for Arabidopsis ) and I didn't found any error at that stage. So forge my genome with BSgenome package and tried to feed PWMEntich by makeBackground function my code look like this

 

    Prom1000bp <- readDNAStringSet("clear_1000_upStream")
    Prom1000bp.genomic.acgt = getBackgroundFrequencies(Prom1000bp)
    pwms.denovo = toPWM(motifs.denovo, prior=Prom1000bp.genomic.acgt)
    # alternatively, any BSgenome object can also be used
     if(require("BSgenome.Nta"))
       bg.logn = makeBackground(pwms.denovo, organism=BSgenome.Nta, type="logn")

and I am getting error like this

Error in getPromoters(organism) :
  Promoter sequences cannot be retrieved automatically for Edwards2017, please provide a set of background sequences explicitely.


I am getting the same error when I trying this code

genome = BSgenome.Nta

genomic.acgt = getBackgroundFrequencies(genome)

 

 

Any help? Thanks.

 

 

r pwmenrich • 798 views
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