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  3. ChIP-seq with Bioconductor in R

Exercise

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.

Instructions

100 XP
  • 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.