gwasglue：将GWAS数据链接到R中的分析工具

# gwasglue <!-- badges: start --> [](https://www.tidyverse.org/lifecycle/#experimental) [](https://travis-ci.org/MRCIEU/gwasglue) [](https://codecov.io/gh/MRCIEU/gwasglue?branch=master) <!-- badges: end --> **Under development** This R package serves as a conduit between packages that can read or query GWAS summary data, and packages that can analyse GWAS summary data. Here is where it lies in the general ecosystem of GWAS data and analysis:  The figure above depicts a set of packages that we plan to connect to. Here is a list of what has been done and what is still to do: #### Data sources - [ieugwasr](https://github.com/mrcieu/ieugwasr) - [gwasvcf](https://github.com/mrcieu/gwasvcf) #### Finemapping - [finemapr](https://github.com/variani/finemapr) - [FINEMAP](http://www.christianbenner.com/) - [PAINTOR](https://github.com/gkichaev/PAINTOR_V3.0) - [CAVIAR](https://github.com/fhormoz/caviar) - [SuSIE](https://stephenslab.github.io/susie-paper/index.html) - TODO - [JAM](https://github.com/pjnewcombe/R2BGLiMS) - TODO #### Colocalisation - [coloc](https://cloud.r-project.org/web/packages/coloc/index.html) - [HEIDI](http://cnsgenomics.com/software/gsmr/) - TODO - [eCAVIAR](https://github.com/fhormoz/caviar) - TODO - [S-Predixcan](https://github.com/hakyimlab/MetaXcan) - TODO #### Mendelian randomization - [TwoSampleMR](https://github.com/mrcieu/TwoSampleMR) - [MendelianRandomization](https://cran.r-project.org/web/packages/MendelianRandomization/index.html) - port from TwoSampleMR - [RadialMR](https://github.com/WSpiller/RadialMR) - port from TwoSampleMR - [MRPRESSO](https://github.com/rondolab/MR-PRESSO) - port from TwoSampleMR - [GSMR](http://cnsgenomics.com/software/gsmr/) - TODO - [MRMix](https://github.com/gqi/MRMix) - TODO #### Visualisation - [gassocplot](https://github.com/jrs95/gassocplot) - Locus zoom plots e.g. [https://github.com/jrs95/gassocplot] - TODO ## Installation You can install the development version of gwasglue with: ``` r devtools::install_github("mrcieu/gwasglue") ``` ## Usage See vignettes etc here: [https://mrcieu.github.io/gwasglue](https://mrcieu.github.io/gwasglue). ## Reference datasets Example GWAS VCF (GIANT 2010 BMI): - http://fileserve.mrcieu.ac.uk/vcf/IEU-a-2.vcf.gz - http://fileserve.mrcieu.ac.uk/vcf/IEU-a-2.vcf.gz.tbi Updated 1000 genomes LD reference panels (multiple populations): - http://fileserve.mrcieu.ac.uk/ld/1kg.v3.tgz 1kg European reference panel for LD (legacy): - http://fileserve.mrcieu.ac.uk/ld/data_maf0.01_rs_ref.tgz 1kg vcf harmonised against human genome reference: - http://fileserve.mrcieu.ac.uk/vcf/1kg_v3_nomult.vcf.gz - http://fileserve.mrcieu.ac.uk/vcf/1kg_v3_nomult.vcf.gz.tbi ## Contributing to the resource For any `<analysis>` package we create a new file called `R/<analysis>.r` which contains two functions: - `gwasvcf_to_<analysis>` - `ieugwasr_to_<analysis>` For an example, see the `R/TwoSampleMR.r` file, which contains the functions `gwasvcf_to_TwoSampleMR` and `ieugwasr_to_TwoSampleMR`.