Retrieving and working with SNPs
SNPs and other polymorphisms are important genomic features and we of the want to retrieve know SNPs in particular genomic regions. In this recipe, we will look at doing that in two different BioMarts that hold different types of data. In the first part, we’ll use gramene to look a retrieving plant SNPs. In the second part, we’ll look at how to find information on human SNPs in the main Ensembl database.
Getting ready
As before, we’ll need only the biomaRt package from Bioconductor and a working internet connection.
How to do it…
Retrieving and working with SNPs can be done using the following steps:
- Get the list of datasets, attributes, and filters from
gramene:library(biomaRt)listMarts(host = "https://ensembl.gramene.org")gramene_connection <- useMart(biomart = "ENSEMBL_MART_PLANT_SNP", ...
