Description
This is the documentation for the in-house Locus Zoom software, developed by Tanya, Matt, and Riku.
If you only need to generate a few plots, you may want to take a look at locuszoom.org instead.
Requirements and prerequisites
Software
You will need the following software to run this tool:
- Latest version of R
- Locus Zoom code from GitHub
bcftoolsplinkversion 1.90 or later
Data
You will need the following data to run this tool:
- Summary level data with the following information:
- Chromosome
- Position
- rsID
- Measure of significance (P or BF)
- 1000 Genomes Project Phase 3 reference data
- UCSC gene region information
Optionally, you may provide the following:
- Output from MAGMA (for colouring the genes based on MAGMA significance)
Table of Content
Before You Begin
1 min read
Requirements and prerequisites Here is a list of requirements that you will need in order to run this tool (relatively) smoothly.
If you have access to the Department of Biochemistry server, you should have little to no problems to meet these …
How to generate LZ plot
3 min read
Make Locus Zoom-like plots with your own LD matrix This script creates an R function to create regional Manhattan plots with points coloured according to LD and genes annotated beneath.
Input file format You will need at least two files to generate a …
Generate multiple LZ plots
5 min read
Make multiple Locus Zoom plots This is a general guide and recommendation on how to make multiple Locus Zooms.
Loop the locus.zoom() call Probably the best way to make multiple Locus Zoom plots is to loop the function call to locus.zoom().
Inputs …
LZ with multiple data sets
3 min read
Stack LZ plots from multiple summary data This page is a general introduction to add multiple “panes” to your LZ plots, using multiple summary data.
Why use multiple summary data? Often we want to overlay LZ plots of the same region from …