echolocatoR is an open-source R library that wraps, integrates and extends several commonly used genetic and functional fine mapping tools, as well as annotation and enrichment tools.
Here, we fine-map loci from recent GWAS to identify causal genetic variants that have been previously associated with Parkinson's Disease (PD) or Alzheimer's Disease (PD).
All data and results can viewed and downloaded via the following interactive Rmarkdown output files below.
git clone https://github.com/RajLabMSSM/Fine_Mapping.git
git submodule init
git submodule update
- Most recent version of fine-mapping, on all 78 loci. Note that currently the plots are shifted over a tab or two from their respective loci (working on fixing this).
- Functional fine-mapping of the LRRK2 locus using PAINTOR.
- eQTL boxplots of selected LRRK2 SNPs using the Fairfax et al. (2014) eQTL summary statistics from monocytes.
- Annotation of all 78 loci usig Biomart and HaploReg.
- Enrichment tests on all 78 loci using fGWAS.
- Enrichment tests on LRRK2 locus using GoShifter.
Currently implemented:
Planning to implement:
- Both Nalls et al. (2019) summary stats and 1000 Genomes Project LD calculations used human genome annotation GRCh37.
- AFA, CAU & HIS subpopulations.
- Monocytes and macrophages.
- expression QTL (eQTL), chromatin QTL (cQTL) and isoform QTL (isoQTL) from Control, Schizophrenia, Bipolar Disorder, and Autism Spectrum Disorder populations.
Brian M. Schilder, Bioinformatician II
Raj Lab
Department of Neuroscience, Icahn School of Medicine at Mount Sinai
