Entering edit mode
Hi everyone.
In the documentation, the value column in minfi::bumphunter output is the average difference level of methylation in the bump. My question is, does this mean that the methylation levels are greater in for example, controls? (If we are comparing control vs case) .
How can I know the meaning of this measure in this case?
Thank you all for your attention
I have this.
g <- as.factor(c(rep("c", 17), rep("t", 40))) # c for controls vs t for tumors matriz <- model.matrix(~ g) # The design matrixThe output after bumphunter:
head(dmrs$table) chr start end value area cluster indexStart indexEnd L clusterL p.value fwer p.valueArea fwerArea 2685 chr18 74961727 74962672 0.2516403 3.271323 88118 424245 424257 13 35 0 0 0 0Thanks for your help
The way you specified your model matrix will by default set the second coefficient to be tumor - control. You can test that by looking at your factor levels (the first factor level is by default the baseline level) or by looking at the design matrix itself.
Thank you very much.