ggplot2 extension for visualising GWAS summary statistics.
Helper functions when working with GWAS (summary) data.
Collection of resources needed in statistical genetics: data, readings, software.
Goal Two approaches Our toy data 1A. A solution that works: ldlink from NIH LDproxy LDmatrix 1B. A solution that almost works: ensembl.org What reference panels/population can we choose from? Access LD between a SNP and its region Access LD matrix Access LD between a SNP and many other SNPs Coloured locuszoom plot 2. Solutions that work half-through SNPsnap API provided by sph.umich 3. A solution that does not work rsnps::ld_search Conclusion Session Info R-packages used:
Goal Getting it done 1. Get summary statistics Visualising associations Identify genomic region with lowest P-value 2. Extracting annotation biomaRt Learning resources Using biomaRt Quick d-tour: assembly GRCh37 or GRCh38? Extracting gene name for one SNP Extracting gene names for genomic region 3. Combining summary statistics and annotation Wouldn’t it be nice… Source In the world of genome-wide association studies (GWAS), we often get a list of genetic markers (SNPs) that seem for some reason relevant for a particular outcome.