I would like to save separately differential binding sites fold>0 and fold<0 reported by 

sum(myDBA.DB$Fold<0)

sum(myDBA.DB$Fold>0) 

I am trying to use the fold option in db.report but it doesn't allow to add > or < . How I can do then this? 

Thanks a lot

Hi Sergio,

You can subset the report to get only the "gain" or "loss" DB sites:

​> myDBA.DB <- dba.report(myDBA.DB)
> myDBA.DB.Gain <- myDBA.DB[myDBA.DB$Fold>0,]
> length(myDBA.DB.Gain)
> myDBA.DB.Loss <- myDBA.DB[myDBA.DB$Fold<0,]
> length(myDBA.DB.Loss)

You can also retrieve the Gain and Loss sites as peaksets in a new "report-based" DBA object using the bDB=TRUE option in dba.report() and setting bGain=TRUE and/or bLoss=TRUE.

Cheers-

Rory

Oh thanks a lot !! 

Sorry Rory, for whatever reason it doesn't save the report in a csv file. I am doing:

myDBA <- dba.contrast(myDBA, group1=myDBA$masks$T1 & myDBA$masks$WT, group2=myDBA$masks$T1 & myDBA$masks$Transgenic, name1="WT:T1", name2="Transgenic:T1")

myDBA.DB <- dba.analyze(myDBA)

myDBA.DB=dba.report(myDBA, bDB=TRUE, bGain=FALSE, bLoss=TRUE, file="myDBA_loss")

When I am writing bDB=TRUE is not saving myDBA_loss.csv , calling myDBA:
2 Samples, 351 sites in matrix (837 total):

If I remove bDB=TRUE is saving myDBA_loss.csv , calling myDBA:

GRanges with 837 ranges and 6 metadata columns:

But this is wrong as it is the whole DB matrix. 

Should include other parameter? Excuse me for being so annoying

Thanks a lot

Hi Sergio-

Indeed if you set bDB=TRUE, dba.report() will create the new DBA object and not save the report file, so you have to call it separately and you are doing. Also, as you say, it will then write out the whole report. You can take the csv report and separate it into two (gain and loss) based on the sign of the Fold column. Alternatively, you can have the report returned, divide it into two as in the example above, and write it out yourself:

​> myDBA.DB <- dba.report(myDBA.DB,DataType=DBA_DATA_FRAME)
> myDBA.DB.Gain <- myDBA.DB[myDBA.DB$Fold>0,]
> write.csv(myDBA.DB.Gain,file=myDBA_gain.csv",row.names=FALSE,quote=FALSE)
> myDBA.DB.Loss <- myDBA.DB[myDBA.DB$Fold<0,]
> write.csv(myDBA.DB.Loss,file=myDBA_loss.csv",row.names=FALSE,quote=FALSE)

Cheers-

Rory