Extracting information in genomic regions of interest
Often, you’ll want to look in more detail at data that falls into a particular genomic region of interest, whether that be the SNPs and variants in a gene or the genes at a particular locus. This common task is handled extremely well by the powerful GRanges and SummarizedExperiment objects. They are a little fiddly to set up but have very flexible subsetting operations that make the effort well worth it. In this recipe, we’ll look at a few ways to set up these objects and a few ways we can manipulate them to get interesting information.
Getting ready
For this recipe, we’ll need the GenomicRanges, SummarizedExperiment, and rtracklayer Bioconductor packages. We will also use a GFF file of features of the Arabidopsis chromosome 4 and a smaller text version of gene features only. These are both in the rbioinfcookbook package, so we’ll extract them from that.
How to do it…
Extracting information...
