Entering edit mode
3.8 years ago
wumeizhen95
•
0
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