BL5631, Practical Analysis of Genomic Data using R
Problem set 2: Genomic Ranges and rtracklayer
Using rtracklayer, BiomaRt, or annotationHub, import into R the human transcripts for GRCh38.
Create a Granges object for the promoters of all protein-coding transcripts, defined for this problem set as 1500 bp upstream of the TSS and 500 bp downstream of the TSS.
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Using the same methods as in 1, create a Granges object of all CpG islands for the human genome.
Calculate the fraction of CpG island annotations that overlap a promoter.
Plot the length distributions for CpG islands that do and do not overlap a promoter.
Upload your R code by 9 October 6:00 PM
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