Hi Rory,
I wonder, if it is possible to extract counting data (after performing dba.count) from a resulting DBA object in csv format where consensus peak names are in the first column, peak positions are in the second/third/forth colums (chromosome, start, end) and normalized number of reads for each sample are in subsequent columns.
Regards
Konstantin
I'm not sure what you mean by consensus peak names? The peak intervals are specified only by their positions, the closest they have t oa name is a number (1:numpeaks).
Here's one way of getting the columns you want in a csv (with the peak number as the peak name):
> normCounts <- dba.peakset(myDBA, bRetrieve=TRUE, DataType=DBA_DATA_FRAME) > write.csv(normCounts, file="normalized_counts.csv")
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version 2.3.6
Thank you very much Rory, that what I need . Regarding peak names, I just was not sure if any peak names (e.g. Peak 1, Peak 2 and so for) were given in addition to coordinates.
Regards
Konstantin
Hi Rory,
Just to clarify, the counts extracted by dba.peakset function, aren't normalized to the library size, aren't they?
Regards
Konstantin
The values to be returned are controlled by the
scoreparameter passed todba.count(). The default values are TMM normalized, which takes library size into account. (You can tell they're normalized because they are not integers).You can change the score without having to re-count the reads by calling
dba.count()withpeaks=NULLandscore=DBA_SCORE_READS(or any of the other scores detailed on thedba.count()man page).