Diffbind data extraction after DE analysis
1
0
Entering edit mode
@jbergenstrahle-12485
Last seen 6.4 years ago

Hi,

I'm currently using Diffbind for my ATAC-seq pipeline. After calling the dba.analyze function you can do various plots via e.g. dba.plotMA. But is there some simple way to extract the logFoldChange, pvalues etc from the DBA object? I guess this should be easy since the object obviously stores the values for plotting, but I just cant seem to find where.

Cheers,

JB

diffbind • 932 views
ADD COMMENT
2
Entering edit mode
Gord Brown ▴ 650
@gord-brown-5664
Last seen 3.2 years ago
United Kingdom

Hi,

dba.report is the function you want.  It has about 20 parameters controlling exactly what you get, but with default parameters (and the dba object) it'll give you p-value, FDR, logFC, etc for the first contrast.  Have a read through the manual for dba.report to see other options.

Cheers,

 - Gord

ADD COMMENT
0
Entering edit mode

Ahh there I go, poorly searched on my side, thanks for the quick answer Gord!

ADD REPLY

Login before adding your answer.

Traffic: 728 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

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

Powered by the version 2.3.6