Good day all,

I have been using Diffbind in R to identify differential peaks in ATACseq data. I have been able to generate contrasts between my 4 groups of samples. However, when I try to output the data, Diffbind defaults to the first contrast.

I have tried:

dba.report(dbObj_analyze, contrast =5)

followed by:

write_tsv (dba_report_filtered_df, "Results/Day0VsDay3nolysis_ATACseq_log2FC.tsv")

or

out <- as.data.frame(res_deseq)
write.table(out, file="results/Day0VsDay3nolysis_ATACseq_log2FC.txt", sep="\t", quote=F, row.names=F)

I must be missing something simple here, but I cant figure it out.

Cheers,
Chris