I am looking for a simple way to extract all of the genes and their coordinates. For transcripts, it is simple to use the trancripts function and directly get a GRanges result. For genes, I thought I could use the select function, but it does not provide the ability to select gene coordinates. The GENCODE annotation GTF file does have gene entries, which seem to be the most extreme coordinates of all transcripts for that gene. Would other users find this a useful option ?
cols(gencode17DB)
[1] "CDSID" "CDSNAME" "CDSCHROM" "CDSSTRAND" "CDSSTART" "CDSEND" "EXONID"
[8] "EXONNAME" "EXONCHROM" "EXONSTRAND" "EXONSTART" "EXONEND" "GENEID" "TXID"
[15] "EXONRANK" "TXNAME" "TXCHROM" "TXSTRAND" "TXSTART" "TXEND"
I have the newest GenomicFeatures and R 3.0.1.
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Dario Strbenac
PhD Student
University of Sydney
Camperdown NSW 2050
Australia