Hi everyone, I want to extrapolate RPKM value from Diffbind. Investigated regions are TSS (± 2.5kb) but around 3500 TSS are "lost" because merged. I have read that in the new version of DiffBind is possible to use dbObj_region$config$mergeOverlap with negative value to avoid merge but I'm not able to use.
Below my code
library(DiffBind) region <- read.csv("DiffBind_template_peaks.csv") DBA <- dba(sampleSheet=region) DBA$config$mergeOverlap = -1 DBA_Count <- dba.count(DBA, score=DBA_SCORE_RPKM) rpkm <- dba.peakset(DBA_Count, bRetrieve=TRUE)
Thanks a lot in advance