Summarising differences in protein binding
The final plot of the differentially bound peaks you'll look at in this lesson is a box plot. This type of plot is useful to summarise the distribution of peak intensities in each sample. DiffBind provides the function dba.plotBox() for this purpose. Box plots highlight the location of the median in different groups as well as the spread of data around it. The plot produced by DiffBind compares the two groups (primary and treatment-resistant tumor) as well as sub-groups consisting of the differentially bound peaks. In addition to the plot itself, dba.plotBox() also returns p-values for the pairwise comparisons between these groups.
As before, the results of the differential binding analysis are available as ar_diff.
This exercise is part of the course
ChIP-seq with Bioconductor in R
Exercise instructions
- Create a box plot of the peak intensities.
- Inspect the returned p-values. Which peak sets are significantly different from each other?
Hands-on interactive exercise
Have a go at this exercise by completing this sample code.
# Create a box plot of the peak intensities
compare_groups <- ___(ar_diff, notch=FALSE)
# Inspect the returned p-values
print(___)