Diffbind: how to get raw read counts and normalized read counts
Hi,
I want to get raw reads and normalized read count from Diffbind. This is my code:
dbObj=dba(sampleSheet = samplesheet)
dbObj=dba.count(dbObj, bUseSummarizeOverlaps=T,bRemoveDuplicates = T)
datac=dba.normalize(datac,normalize=DBA_NORM_LIB)
Then I want to get normalized read count dataframe from this. I try to read this quesion and official manuals.So I write following code:
rawread=dba.peakset(datac,bRetrieve = T,DataType = DBA_DATA_FRAME,writeFile = 'rawread.csv',peak.format ='csv' )
I get a dataframe:
So is it right? Or how can I get raw read counts and normalized read counts?
1 answer
Yes, these are the normalized reads.
If you want to get the raw read counts, you can change the reported score and then re-retrieve the binding matrix:
normread <- dba.peakset(datac, bRetrieve = TRUE, DataType = DBA_DATA_FRAME, writeFile = 'normread.txt')
datac <- dba.count(datac, peaks=NULL, score=DBA_SCORE_READS)
rawread <- dba.peakset(datac, bRetrieve = TRUE, DataType = DBA_DATA_FRAME, writeFile = 'rawread.txt' )
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Rory Stark
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