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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Wojeff • 0
@wojeff-14309
Last seen 14 months ago

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?

genomicranges genomicfeatures promoter upstream_flank • 533 views
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