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.