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 focus on the molecular relationship between genetic variation and phenotypic expression.

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How do I fetch lincRNAs from Ensembl?

Here's a very short post on how to fetch lincRNAs from Ensembl using R and the biomaRt package. For those who are not familiar with biomaRt, you can check out my older post on biomaRt. Firstly, start R and install the biomaRt package from Bioconductor by copying and pasting the code below:

source("http://bioconductor.org/biocLite.R")
biocLite("biomaRt")

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Thoughts on converting gene identifiers

If you've worked in the genomics field, then you've most likely spent some time converting gene identifiers to other gene identifiers or to gene symbols. Some common gene annotation databases include RefSeq, UCSC known genes, Entrez gene and Ensembl genes. In the past, I've relied on large tables that provide the lookup between different identifiers, such as the gene2refseq.gz file that provides lookups between Entrez gene IDs to RefSeq IDs.

However, more elegant and robust solutions exist such as BioMart, which is a freely available online service that allows you to download genomic annotations from several databases. The usefulness of the service is that you can easily perform lookups between several different databases, i.e. converting gene identifiers. There's a Perl package for working with BioMart and a R Bioconductor package. For this post, I will be using the R Bioconductor biomaRt package; I've previously written a short guide on learning to use biomaRt for those interested in a short introduction. The crux of biomaRt is summarised in the biomaRt vignette:

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Learning to use biomaRt

In the past I've been manually downloading tables of data annoation and parsing them with Perl. I guess it's time to do things more elegantly. Below is code taken from the biomaRt vignette:

Note
If you are using Ubuntu and getting a "Cannot find xml2-config" problem while installing XML, a prequisite to biomaRt, try installing libxml2-dev:

sudo apt-get install libxml2-dev

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