After using dba. analyze() to calculate the difference, use dba. report() to extract the difference peak, but the difference peak coordinates have been merged. How to output the real peak coordinates corresponding to each difference peak in different sample species?
> library(DiffBind)
> dbObj_S3_S2 <-dba(sampleSheet="D5_D3_Linux.csv")
> dbObj_S3_S2 <- dba.count(dbObj_S3_S2 , bUseSummarizeOverlaps=TRUE)
> dbObj_S3_S2 <- dba.normalize(dbObj_S3_S2)
> dbObj_S3_S2 <- dba.contrast(dbObj_S3_S2,reorderMeta=list(Condition="S2"),minMembers = 2)
> dbObj_S3_S2 <- dba.analyze(dbObj_S3_S2, method=DBA_ALL_METHODS)
> comp1.deseq2_S3_S2 <- dba.report(dbObj_S3_S2, method=DBA_DESEQ2,contrast=1,th=1)
•
written
by
441559287 •
1 answer
I'm not sure what you mean by "real" peak coordinates.
Do you mean the overlapping peak calls in each sample that contributed to the consensus peak? In that case there can be multiple "real" peak coordinates for each consensus peak. You can identify these by overlapping the consensus peaks returned by dba.report() with each individual peakset. The easiest way to do that is to load the individual peaksets as GRanges objects (as is the returned report).
Log in to answer this question.
-
Diffbind and DESeq2 comparison for differential sites
written by Ankit
-
Multi-factor designs in DiffBind
written by g.persic1991 •
-
diffbind dba.report error
written by jellybean5 •
-
DiffBind 3.2 error
written by Huang Zhihao •
-
why DiffBind, diffferentially binding site is the for different samples
written by iridha •
-
Diffbind-edgeR or Deseq2
written by francesca3 •
-
DiffBind Issue with coordinates
written by aboyd003 •
-
DiffBind without replicates
written by zhangdengwei
-
Different options tryed with DiffBind and did not know what final result believe
written by iraia.munoa
-
Huge difference between differential peaks with EdgeR and DESeq2 using Diffbind
written by daniele.avancini •
