Biomart: Finding Ensembl Repeat Regions In A List Of Coordinates From R

Question

[Danielsbrewer]

I am using R and I have got a list of regions:

Chr  Start   Stop
1    1289    110000
...

What I would like to know is whether there are any repeat regions in each of the list of regions. Ensembl has information on the repeats but I can't find a way of grabbing this information easily from within R. Normally I would use BiomaRt to query ensembl but I can't find the appropriate attribute. Has anyone got an idea of how to do this?

Answer 1

[Gareth Palidwor]

The simplest way would be to download a list of RepeatMasker determined repeat ranges from UCSC Table Browser, then intersect those with your set of regions using IRanges. It's not clear what genome you're using but UCSC has repeat regions for quite a few.

**edited; accidentally said BioMart instead of Table Browser for UCSC

Answer 2

[Neilfws]

I don't see a way to access repeats using BioMart. Perhaps because the focus of BioMart is gene-associated features.

I'd recommend using either the UCSC tables, as Gareth said, or the Ensembl API. The latter has methods for retrieving repeat features from a genome sequence slice.