I'm trying to estimate the methylation of the cg sites located on the promoters of some genes.
So i have a csv with the cgsites and their beta.
I have a list of genes. now I'm trying to find the promoters of said genes.
Taking for example "TSPAN6", going to the ensemble website, I see the promoter tagged as
Stable ID ENSR00000911389 Type Promoter Core bp Chromosome X: 100,635,001-100,637,600
I tried in R:
promoters(EnsDb.Hsapiens.v86, filter = GeneNameFilter("TSPAN6"))
but it doesn't show this information
I also tried the biomart package:
regulation <- useEnsembl(biomart="regulation", dataset="hsapiens_regulatory_feature") reg.attr <- listAttributes(regulation) test.promo <- getBM(attributes = reg.attr$name, filters = 'regulatory_stable_id', values = "ENSR00000911389", mart = regulation)
but I can't find a field to relate the promoter to the gene...
In each case it seems i'm getting the transcripts (ie ENST*) associated to TSPAN6, but I need the start and end of the promoter so i can filter my cgsites/beta.
Anyone could please advise how to achieve that?