Computational biology and genomics
The American College of Medical Genetics and Genomics (ACMG) have recommended that genetic variants that may be pathogenic or likely pathogenic in certain genes should be reported back to the patient. The latest list of genes can be found here. How do I assess whether a variant is pathogenic or likely pathogenic? Use this tool,...
I'm a fan of GEMINI and have been using it for for a year and a half for various exome projects. I have written two scripts that can generate variant summaries from a GEMINI database. I prefer bar plots over the pie charts created by VEP. A summary pie chart created by VEP.
The diagram package makes it easy to create flowcharts in R. In this post I'll show an example of creating a simple flowchart. The most important part is to understand how the coordinate systems works; once you understand that, it's just a matter of placing your arrows and boxes accordingly to create your flowchart. To...
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...
An adjacency list is simply an unordered list that describes connections between vertices. It's a commonly used input format for graphs. In this post, I use the melt() function from the reshape2 package to create an adjacency list from a correlation matrix. I use the geneData dataset, which consists of real but anonymised microarray expression...
Just recently, the genome Aggregation Database (gnomAD) VCF files were available for download: The long-awaited gnomAD VCF is here - sites + frequencies for 123,136 exomes and 15,496 genomes: https://t.co/8puaTvJ45w pic.twitter.com/sxKOEVFDml — Daniel MacArthur (@dgmacarthur) February 27, 2017
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...