Hi,

When I run dba.counts, it showed an error below (fig1):

Error in pv.counts(DBA, peaks = peaks, minOverlap = minOverlap, defaultScore = score,  : Some read files could not be accessed. See warnings for details. In addition: Warning message: not accessible

Is it because that I don’t have bamControl for 6 ATAC-Seq samples (fig2)? How can I overcome this issue? Thank you so much.

Best,

Gary

fig1

fig2

Hi Gary-

Looks like a bug in the case where some samples have control and some do not. I have checked in a fix, it will take a few days to be updatable as version 2.0.5.

In the meantime, here is a workaround you can call before dba.count():

> scale$class[11,scale$class[11,]==""] <- NA
> scale <- dba.count(scale, minOverlap=2)

Cheers-

Rory