2.8 years ago by
China/Guangzhou/Southern Medical University
5'UTR is extracted by fiveUTRsByTranscript(TXDB) and 3'UTR is extracted by threeUTRsByTranscript(TXDB). These two functions are defined in GenomicFeatures package and the information is already available in TXDB object. ChIPseeker doesn't define them.
For intergenic region, it means the peak doesn't overlap with any genes.
For the end of the gene, we didn't define it. What we defined that related to the end of the gene is the 'Downstream'. Downstream is the immediate downstream of the gene end. If the peak is located at upstream of the gene end, it is actually inside the gene and will be annotated as overlap with extron or intron.