Peaks vs background
Now it is time to compare the coverage distribution of peaks, blacklisted regions, and background. In this exercise, you will examine data from chromosome 5.
The binned read counts for peaks, blacklisted regions, and background for this chromosome are available as peak_bins, bl_bins, and
bkg_bins respectively. The score column contains the read counts.
It may take a moment to load all required data and R packages for this exercise. Please be patient.
This exercise is part of the course
ChIP-seq with Bioconductor in R
Exercise instructions
- Prepare read counts for plotting by organizing them in data frames.
- Combine the three data frames using
rbind(). - Create a boxplot of the read counts by bin type.
Hands-on interactive exercise
Have a go at this exercise by completing this sample code.
# Prepare read counts for plotting by organising them in data frames
peak_scores <- data.frame(source="peaks", fragments=___$score)
bl_scores <- data.frame(source="blacklist", fragments=___)
bkg_scores <- data.frame(source="background", fragments=___)
scores <- rbind(___, ___, ___)
# Create a boxplot of the read counts by bin type
ggplot(___, aes(y=fragments, x=source)) + geom_boxplot()