What will be the best use of the dba.peakset and minOverlap to extract 3 datasets that have the common peaks, the peaks enriched in c-Jun ChIP and the ones enriched in JunB ChIP. my dataset looks like:
CHIP_seq_Goett_peaks_ALL 4 Samples, 33031 sites in matrix: ID Tissue Factor Condition Replicate Caller Intervals FRiP 1 Cell1px8 epithelial junB Cell1_junB 1 counts 33031 0.12 2 Cell1px13 epithelial junB Cell1_junB 2 counts 33031 0.13 3 Cellc1px13 mesenchymal cJun Cellc1_cJun 1 counts 33031 0.04 4 Cellc1px8_13 mesenchymal cJun Cellc1_cJun 2 counts 33031 0.08 1 Contrast: Group1 Members1 Group2 Members2 DB.edgeR DB.DESeq2 1 junB 2 cJun 2 13259 10837
I've seen people Using values as 0.7, but I do not understand the usage and why the default value is 2. Also, how can this be changed to my specific needs?
One other thing I noticed that even I do
ChIPpeakset <- dba.peakset(CHIP_seq_Goett_peaks_ALL, minOverlap = 0.7)
I get the following:
> ChIPpeakset$minOverlap  2
Thank you in advance.