Annotating peaks
In the previous exercises, you created a table of merged peak calls from all samples (available here as peaks_merged) and a table with gene annotations (available as human_genes). Now it is time to combine information from both tables using the annoPeaks() function provided by the ChIPpeakAnno package. For each peak that is sufficiently close to the start site of a gene (as determined by the bindingRegion argument), this function will return detailed information on the gene in question in a data frame. This includes a column, insideFeature, indicating where the peak is located relative to the gene.
This exercise is part of the course
ChIP-seq with Bioconductor in R
Exercise instructions
- Annotate peaks with the closest gene.
- Determine the number of peaks that were annotated with genes.
- Create a summary table indicating where peaks were located relative to genes.
Hands-on interactive exercise
Have a go at this exercise by completing this sample code.
# Annotate peaks with closest gene
peak_anno <- ___(peaks_merged, human_genes, bindingType="startSite", bindingRegion=c(-5000,5000))
# How many peaks were found close to genes?
length(___)
# Where are peaks located relative to genes?
table(peak_anno$___)