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
[1] 2
Thank you in advance.
Hi Rory, thank you getting back at me. this dataset has already been under count/contrast/analyze, so your assumption is correct. the scripts you provided worked.
this work perfectly.
I am probably confused or did not comprehend the following part from the tutorial
The specified part did not work with my list. Do I need to reprocess the initial list without the count/contrast/analyze part?
Thank you
And another question will be: if I would like to include to the resistant/ responsive only the ones that are foe example above fold change of 2 ( the Fold in your case is log2?) how could I accomplish that? Over all this is something that is been done in the Volcano plots.