Shiny interface to explore patterns of LD. Visualisations include:
- a heatmap of all pairwise-LD between SNPs within a user-defined loci
- a dendrogram of the same
- a customised 'locus zoom-like' plot, which we call LDZoom.
The Shiny app lives in the LDExplorer directory of this repo. After cloning this repo to your own system, you can begin exploring as follows:
- Run the Shiny app (choose your favourite method)
- On the HOME page enter the chromosome and region (start, end in base pairs) for your region of interest (loci). Click on Calculate LD.
- Go to the Ld Proximity page. This will begin downloading the 1000 Genomes data for your loci, calculate the LD and display the heatmap and dendrogram.
- After (3), you can then go to the LDZoom page. Enter a leadSNP, adjust the LD threshold (if required) and click on Visualise LD. An LDZoom and summary table will be displayed.
Obviously, you will need R and Shiny. In addition you will need the GLIDA package. GLIDA was developed to help explore patterns of LD, and can be installed from GitHub using devtools:
library(devtools)
devtools::install_github("glida", "nickb-")GLIDA has a number of dependecies, which should be automatically installed alongside GLIDA.
The LDExplorer app is being actively developed. We are working on fixes to the following:
ISSUE #1: Currently the "calculate LD" button on the HOME tab does not begin downloading and pre-processing of 1000 Genomes data. Users need to navigate to the LDProximity tab to begin this. Download should happen as soon as the user clicks on "Calculate LD".
ISSUE #2: Everytime the user restarts the app and enters the details for a loci, this region is downloaded from 1000 Genomes. There should be a check to see if the data already exists and if so, do not download again.
ISSUE #3: glida::ldPopulation() is throwing an unexpected EOF warning. This needs to be investigated, but is non-critical.
The LDExplorer and GLIDA tools are actively maintained by the Merriman Lab at the University of Otago. We welcome feedback and contributions from users. Please contact nick.burns@otago.ac.nz.