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.
Deze oefening maakt deel uit van de cursus
ChIP-seq with Bioconductor in R
Oefeninstructies
- Examine the
ar_bindingobject to confirm that it contains the required contrast. - Run the differential binding analysis.
- Examine the result.
Praktische interactieve oefening
Probeer deze oefening eens door deze voorbeeldcode in te vullen.
# 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(___)