Gene to OMIM phenotype

A couple of weeks ago, I wrote a post on identifying OMIM phenotypes that are associated with a gene of interest. I thought I solved the problem by using one of my favourite R packages (biomaRt) but alas. For example, I could not find any OMIM IDs associated with the TTN gene using biomaRt. In...

Continue Reading

Gene to OMIM Morbid Map

Update 2017 May 10th: I realised that this approach doesn't work for all genes, unfortunately. For example, the gene TTN (which is an HGNC approved gene symbol) is associated with 600334, 603689, 604145, 608807, 611705, and 613765 but biomaRt returns an NA. Please refer to an updated post. I was interested in the number of...

Continue Reading

Getting started with the OMIM API

Updated 2016 September 15th: I've made this into an R package, which is available at my GitHub repository A short post on utilising the OMIM API via some wrapper functions I wrote in R. A wrapper, as explained in the Wikipedia article, is simply a subroutine that calls another subroutine. If you plan on using...

Continue Reading

OMIM IDs to gene coordinates

A post on linking OMIM IDs to gene coordinates using biomaRt; this provides a way of representing OMIM IDs on the genome. For those unfamiliar with OMIM, here's the description from the OMIM FAQ: Online Mendelian Inheritance in Man (OMIM) is a continuously updated catalog of human genes and genetic disorders and traits, with particular...

Continue Reading