Peak calls
Reads are scattered all across the genome, but locations bound by the protein of interest will attract many overlapping reads, leading to peaks in coverage. These peaks are typically recorded with their genomic coordinates as well as a score that indicates the strength of the signal observed for this peak.
A set of peak calls has been loaded into R for you. The peak calls are stored in a GenomicRanges object called peaks. In addition to the usual functions to access the content of GenomicRanges objects, two convenience functions are available for peak calls. You can use the chrom function to obtain the chromosome a peak is located on and the score function to obtain its score.
Este ejercicio forma parte del curso
ChIP-seq with Bioconductor in R
Instrucciones del ejercicio
- Print a summary of
peaks. - Use the
score()function to find the index of the highest scoring peak. - Extract the genomic coordinates of the highest scoring peak using the
chrom()andranges()functions.
Ejercicio interactivo práctico
Prueba este ejercicio y completa el código de muestra.
# Print a summary of the 'peaks' object
print(___)
# Use the score function to find the index of the highest scoring peak
max_idx <- which.max(___(peaks))
# Extract the genomic coordinates of the highest scoring peak using the `chrom` and `ranges` functions
max_peak_chrom <- ___(peaks)[___]
max_peak_range <- ___