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extend getPromoters() #16

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GuangchuangYu opened this Issue Oct 19, 2015 · 3 comments

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GuangchuangYu commented Oct 19, 2015

getPromoters() function prepare a GRanges object of promoter regions by user specify upstream and downstream distance from Transcript Start Site (TSS).

Refer to the questions in Bioconductor support site: https://support.bioconductor.org/p/73069/#73157 and https://support.bioconductor.org/p/73377/, some users (studying RNA splicing I guess) may interesting in how protein binding to the start of intron/exon.

getPromoters() function will extend to support output a GRanges object of Intron/Exon start region similar to Transcript start region.

Maybe the function name should be changed.

@GuangchuangYu GuangchuangYu changed the title extend `getPromoters()` extend getPromoters() Oct 19, 2015

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GuangchuangYu commented Oct 19, 2015

@Puriney do you have any recommendation of the new function name? or we just use the getPromoters() for all types?

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Puriney commented Oct 19, 2015

getBioRegion(..., by = c('gene', 'transcript', 'promoter', 'exon','intron'))
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GuangchuangYu commented Oct 20, 2015

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