TADCompare result

[caokai001]

Hi author!
At your suggestion, I installed the TADCompare tool,I run my two sample,command like this.

TD_Compare <- TADCompare(Treat_matrix, Control_matrix, resolution = 40000)

I selected a few split positions and visualized them with a juicerbox, but the display is not Significant differences, what should I do?

Hope to get your advice.
Thanks!

[mdozmorov]

It is hard to see at this zoom level. As a first step, try TADCompare native visualization, https://bioconductor.org/packages/devel/bioc/vignettes/TADCompare/inst/doc/TADCompare.html#visualization. It's not perfect, but you can see exactly what is going on with the boundary score in each matrix at this location.

[caokai001]

Hi mdozmorov ,
I'm very happy to have received your response.

I use DiffPlot function to plot this region(25M-27M) , so the yellow location is 25.6M position. it is marked as split case.
The figure below shows the 25-27M region(z_thresh=2)

Next, Modified the threshold parameter (z_thresh=4)，

TD_Compare2 <- TADCompare(Con_matrix, VX765_matrix, resolution = 40000, z_thresh = 4) 

this is TAD_compare result of 52M-54M, z_thresh is 4. can see that 53040000 is merge case.

52440000	-3.24466009403347	0.488758712173734	2.10029595493549	"Non-Differential"	"Matrix 2"	"Non-Differential"
52560000	1.45637750465065	3.3081229307757	2.15435166251112	"Non-Differential"	"Matrix 1"	"Non-Differential"
52840000	-1.78144253713954	1.42173535127505	2.16579425801131	"Non-Differential"	"Matrix 2"	"Non-Differential"
53040000	-4.60372491414654	-0.299394268138185	2.1083055914697	"Differential"	"Matrix 2"	"Merge"
53240000	1.65752167793198	1.79574654614811	0.722915668604286	"Non-Differential"	"Matrix 1"	"Non-Differential"
53280000	-3.02726589892429	3.78269009092189	4.88033123774187	"Non-Differential"	"Matrix 2"	"Non-Differential"
53320000	-1.8895274929546	1.90796272265606	2.64836165379702	"Non-Differential"	"Matrix 2"	"Non-Differential"
53720000	0.103712131200207	1.63487396200186	1.38196887724348	"Non-Differential"	"Matrix 1"	"Non-Differential"
53760000	-3.08892607800212	2.70083590121561	3.96224349218883	"Non-Differential"	"Matrix 2"	"Non-Differential"

so I use Diffplot to show this region, look at yellow dot.

I don’t know why it’s not obvious!

Thanks!