I am using DiffBind to analyze differential transcription factor binding in some data I have and I keep getting the message as a result of dba.analyze(myData): "No correlation heatmap plotted -- contrast 1 does not have enough differentially bound sites."
I looked at the source code on github (DBA.R: lines 551 - 565) and was wondering if there is a way to get dba.analyze() to return an object of all differentially bound sites even if their p-values do not meet the cutoff? Would I just change line 553 "th = 0.05" to whatever threshold I choose?
My output from sessionInfo() is: R version 3.1.2 (2014-10-31); Platform: x86_64-unknown-linux-gnu (64-bit) ....
other attached packages:
 DiffBind_1.12.3 GenomicAlignments_1.2.2 Rsamtools_1.18.3
 Biostrings_2.34.1 XVector_0.6.0 limma_3.22.7
 GenomicRanges_1.18.4 GenomeInfoDb_1.2.5 IRanges_2.0.1
 S4Vectors_0.4.0 BiocGenerics_0.12.1 ...
Would appreciate your help! Thanks,