ggplot2 extension for visualising GWAS summary statistics.
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 Get started Data Add geographical coordinates Create leaflet Save the map Reason for deviation from the original This post provides the R-Code to map the 26 populations of the 1000 Genomes project.
Goal Create a map similar to the one1 on the front page of http://www.internationalgenome.org/ in a reproducible manner.
Version on internationalgenome.org
Get started Packages needed:
## accessed via :: # library(mapview) # library(readxl) # library(readr) # library(purrr) # library(tidyr) # library(forcats) library(leaflet) library(dplyr) library(ggmap) ## for geocode, devtools::install_github("dkahle/ggmap") ggmap requires a google map api key2:
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.