<p>Note that the annotation file differ from that you would get from FlyBase; I have had to edit the annotation file to add chr in front of the chromosome names and to change the mitochondria name to chrM; since the data in the BAM file I used later on follow these conventions.</p>
<p>The <em>feature</em> parameter defines which feature to look for in the provided file. Commonly mRNA for gff3 and transcript for gtf. It defaults to mRNA. Several parameter can ge given as argument.</p>
<p>The <em>output</em> paramter defines the type of object that is returned. It can generate a <strong>Genome_intervals</strong> or a <strong>GRanges</strong> class of objects. The former can be saved as a gff3 using the writeGff3 function from the genomeIntervals package (loaded). The latter can be saved as an RData object and/or be used directly in the construction of an AnnotParam.</p>