R-package which allows the user to fit structural equation models based on the summary statistics obtained from genome wide association studies (GWAS). Until explicitly stated otherwise the code on this github is an alpha version (now on version 0.0.3d) and under active development. The code may thus produce undesired results on certain operating systems or when run concurrently with specific packages or R versions. Feel free to raise issues if (or when...) the package produces undesired results, we will attempt to swiftly deal with known issues. Please visit the wiki to get started, or check out the paper. If you are having issues and not finding the answers anywhere on the wiki or FAQs page, we encourage you to post your question on the google group.
Feature update: GenomicSEM can now run HDL a novel method for estimating heritability and genetic correlation that can in some cases outperform LDSC. See out tutorial HERE
Code Update: The most recent code update is dated April 12th, 2021. This code update includes a statistically equivalent, but far more efficient, way of calculating model chi-square. In the context of a userGWAS model where model chi-square was requested this may decrease run-times by ~50%. We recommend reinstalling to the most recent update of GenomicSEM. However, please note that changes in Genomic SEM defaults are likely to produce slight changes in results relative to previous versions. For further details, see version history
PGC worldwide lab meeting on genomicSEM
Click below for a video which provides a very clear introduction to the method/paper:
Contents of the wiki:
Learn how to install GenomicSEM
Consider some of the nuances of summary data, and know where to find summary data.
Fit SEM models to GWAS summary data without a SNP
Run a GWAS where the SNP is included in the structural equation model.
Estimate functional enrichment for any parameter in a Genomic SEM model (e.g., factor variances).
Run multivariate TWAS using T-SEM
Installation:
We assume you are running R 3.4.1 or newer. We guarantee no backward or forward comparability. If something breaks please raise the issue on GitHub and we will try and fix it ASAP.
First, you need to install the devtools package. You can do this from CRAN, launch R and then type
install.packages("devtools")
Load the devtools package.
library(devtools)
Now you are ready to install the latest version of GenomicSEM. Note that this will often raise 24 warnings about replacing previous imports; these warnings are safe to ignore.
install_github("GenomicSEM/GenomicSEM")
That's it! You are ready to start using GenomicSEM
License
Copyright (C) 2018 Andrew Grotzinger, Mijke Rhemtulla, Hill F. Ip, Michel Nivard, & Elliot Tucker-Drob
This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
You should have received a copy of the GNU General Public License along with this program. If not, see https://www.gnu.org/licenses/.