Hi

I am trying to use PWMEnrich to look for promoter enrichment in a group of Arabidopsis genes.

As the Arabidopsis genome is not supported I am trying to create the relevant backgrounds etc

I tried the command bellow and got the following:

> genomic.acgt = getBackgroundFrequencies(BSgenome.Athaliana.TAIR.TAIR9)
Error in getPromoters(organism) : 
  Promoter sequences cannot be retrieved automatically for TAIR9, please provide a set of background sequences explicitely.

I then built  a DNAStringSet of promoters of the Arabidopsis Genome (Prom1000bp) and tried this:

 > Prom1000bp.genomic.acgt = getBackgroundFrequencies(Prom1000bp)
Error in getPromoters(organism) : 
  The input parameter needs to be a valid genome name ('dm3', 'mm9' or 'hg19') or a set of background sequences.

My question is what structure is "a set of background sequences" if they are not a DNAStringSet?

Hi,

This function should be taking a set of background sequences, but isn't. It will be fixed in the next release, thanks for the report!

Until then, this function will give you an equivalent output (it's what getBackgroundFrequencies is internally calling):

Prom1000bp.genomic.acgt = makePriors(Prom1000bp, 1)

Cheers, Robert

Hi,

This function should be taking a set of background sequences, but isn't. It will be fixed in the next release, thanks for the report!

Until then, this function will give you an equivalent output (it's what getBackgroundFrequencies is internally calling):

Prom1000bp.genomic.acgt = makePriors(Prom1000bp, 1)

Cheers, Robert

That is great thanks