Fitting the model
Now you are ready to carry out the differential binding analysis. This will tell which of the peaks differ significantly in intensity between the two tumor types. Knowing which peaks differ between groups will form the basis of further analysis that aims to determine the underlying mechanisms driving these differences. For now, let's look at finding the differentially bound peaks. The dba.analyze() function from the DiffBind allows you to do this. In the previous exercise, you established the contrast for the comparison between tumor types. Using the object with the contrast, you can simply call dba.analyze() to do the remaining work.
This exercise is part of the course
ChIP-seq with Bioconductor in R
Exercise instructions
- Examine the
ar_bindingobject to confirm that it contains the required contrast. - Run the differential binding analysis.
- Examine the result.
Hands-on interactive exercise
Have a go at this exercise by completing this sample code.
# Examine the `ar_binding` object to confirm that it contains the required contrast
print(___)
# Run the differential binding analysis
ar_diff <- ___(ar_binding)
# Examine the result
print(___)