Failed to get promoters using promoters() in R 4.0.3.
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Arslan • 0
@b9531c68
Last seen 23 hours ago
Pakistan

I am trying to get the promotors region using the following code but got an error.

query_ref <- ucscTableQuery(session, track="RefSeq Genes",table="refGene",
                        range=GRangesForUCSCGenome("mm9", "chr12"))

prom.refgene <- promoters(query_ref, upstream = 1000, downstream = 1000, use.names = FALSE)

Error in (function (classes, fdef, mtable) : unable to find an inherited method for function ‘promoters’ for signature ‘"UCSCTableQuery"’
promoter GenomicRanges rtracklayer GRanges • 136 views
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shepherl 2.8k
@lshep
Last seen 1 day ago
United States

This probably should have been labelled with rtracklayer rather than GRanges. The ucscTableQuery function creates an ucscTableQuery instance not a GRanges object to be able to use promoters directly. I think you have to use one of other helper functions listed in ?UCSCTableQuery first to convert it. Something like tracks or getTable

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Thanks for the suggestion, I did it using track() function.

prom.refgene <- promoters(track(query_ref), upstream = 1000, downstream = 1000, use.names = FALSE)
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