Question: GenomicFeatures: How to extract a gene's upstream region of TSS up to the end position of the flanking (nearby) gene.
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12 months ago by
wuzefeng20080 wrote:

Hi there, I wanted to extract the TSS up-stream region of each gene up to the end position (TTS) of the nearby gene. I only known the promoter function, but it seems can not deal with this problem. I could only get the GenomicRange object of  all genes from the gtf file by the following codes:

txDB <- makeTxDbFromGFF("test.gtf")

genes <-genes(txDB)

How to obtain my desired region for each gene?