R Bioinformatics Cookbook

How it works...

Step 1 starts by loading in our pre-prepared RangedSummarized experiment; note that the names slot of the GRanges object in there is not populated. We next create a custom function, make_tag(), which works by pasting together seqnames, starts and the computed end (start + width) from a passed GRanges object. Note the @ sign syntax: this is used because GRange is an S4 object and the slots are accessed with @ rather than the more familiar $.

In step 2, the code pulls out the actual data from RangedSummarizedExperiment using the assay() function. The matrix returned has no row names, which is unuseful, so we use the if clause to check the names slot—we use that as row names if it's available; if it, isn't we make a row name ...