DiffBind: How could I debug estimateDispersionsFit (required by DBA_DESEQ2)
0
0
Entering edit mode
@zhaolin20042008-12777
Last seen 3.7 years ago
U of Michigan

Hi,

I got an error when I used DiffBind to treat a human ATAC-seq library data set. (see  https://support.bioconductor.org/p/94915/).ATAC-seq is the data set like DNase-seq, the enrichment of open chromatin region are variable.

Error in estimateDispersionsFit(object, fitType = fitType, quiet = quiet) :
all gene-wise dispersion estimates are within 2 orders of magnitude
from the minimum value, and so the standard curve fitting techniques will not work.
You can instead use the gene-wise estimates as final estimates:
dds <- estimateDispersionsGeneEst(dds)
dispersions(dds) <- mcols(dds)\$dispGeneEst

I knew the reason but I failed to debug using trace () at DBA_DESEQ2 because it is not a function.Could anyone suggest a solution? Thanks a lot.

atac-seq diffbind • 784 views
1
Entering edit mode

Hi,

If you want to debug estimateDispersionsFit you can debug it directly:

> debug(DESeq2::estimateDispersionsFit)

> x = dba.analyze(...)

Then use the debug commands to step through it, when R stops in that function.

Traffic: 194 users visited in the last hour
FAQ
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.