Hi,

I have a list of differentially bound sites between conditions and would like to export lists defined by 2 things: fold change between some positive or negative value given the condition and specific FDR cutoffs. If anyone has advice on how to go about this would be huge help, thanks so much! 

Rob

In DiffBind, the main way to export lists of differentially bound sites is via the dba.report() function. You can specify a maximum FDR value, as well as a minimal fold change (in log2 form). You can retrieve the data as a GRanges object or a dataframe, and you can export it in a csv file using the file parameter.

You can also retrieve all the data by setting th=1, then use R to filter what you want. For example:

> data(tamoxifen_analysis)
> tamData <- dba.report(tamoxifen,th=1)
> tamData[tamData$FDR<.01,]
> tamData[tamData$Fold>1,]

-Rory