get raw reads count from dba.peakset
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15 months ago

I want to get normlized matrix from diffbind, But get interger number. not resaonable

> dbpeak<-dba.peakset(dbcount,bRetrieve=TRUE)
> dbpeakDF<-data.frame(dbpeak)
> head(dbpeakDF)
  seqnames  start    end width strand    X10N.1    X10T.1      X10N      X10T
1     chr1 629697 630197   501      * 247.68300 1058.0486 247.68300 1058.0486
2     chr1 630236 630736   501      * 196.59434  713.8641 196.59434  713.8641
3     chr1 630946 631446   501      * 607.24371 2398.6685 607.24371 2398.6685
4     chr1 631850 632350   501      *  25.86768  123.2265  25.86768  123.2265
5     chr1 632755 633255   501      * 149.38583  590.6376 149.38583  590.6376
6     chr1 633276 633776   501      * 118.99131  433.4175 118.99131  433.4175

then i re-calculate, but the result is interger number.I thought "DBA_SCORE_TMM_MINUS_FULL_CPM" is the return CPM value, which should be float. Am I wrong?

ori_dba<-dba(sampleSheet=filename)
> dbcount1<-dba.count(ori_dba,bParallel=TRUE,summits=250,score='DBA_SCORE_TMM_MINUS_FULL_CPM')
Re-centering peaks...
> dbpeak1<-dba.peakset(dbcount1,bRetrieve=TRUE)
> dbpeakDF1<-data.frame(dbpeak1)
> head(dbpeakDF1)
  seqnames  start    end width strand X10N.1 X10T.1 X10N X10T
1     chr1 629697 630197   501      *    383    498  383  498
2     chr1 630236 630736   501      *    304    336  304  336
3     chr1 630946 631446   501      *    939   1129  939 1129
4     chr1 631850 632350   501      *     40     58   40   58
5     chr1 632755 633255   501      *    231    278  231  278
6     chr1 633276 633776   501      *    184    204  184  204
ATAC-seq • 285 views
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