Hi, I would like to know how to change the default P value and FDR cutoff in DiffBind if I use DBA_DESEQ2 for the differential analysis? Thanks a lot!
p-value cutoff is specified in the entry dba.object$config$th. You can directly change it
dba.object$config$th <- .01
The th and fold parameters in the dba.report function are what you need to tweak.
By default the threshold is set with FDR, so changing the th value will change the FDR threshold.
To use p-value instead, use this option after generating your object using dba
MyDbaObject$config$bUsePval <- TRUE
same way you can also change the p-value threshold next
MyDbaObject$config$th <- 0.01
then continue the analysis with normalizing and reading the counts etc.
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