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Select traits
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Get instruments for traits
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Extract SNPs from outcomes
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Harmonise data
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Perform MR
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Upload to neo4j
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Add new traits
- add to existing traits
- get instruments and find unique instruments
- extract all outcome SNPs for new trait, and new instruments from other traits
- harmonise data
- perform MR
- upload to neo4j
need two files
- node information
- mr estimates
- heterogeneity stats
neo4j
to run in background:
docker run -d --publish=7474:7474 --volume=$HOME/neo4j/data:/data neo4j:2.3 docker exec -i -t neo4j:2.3 /bin/bash
./neo4j-import
--into mr-eve.db
--id-type string
--nodes:gene ../data/upload/genes.csv
--nodes:snp ../data/upload/snps.csv
--nodes:trait ../data/upload/traits.csv
--relationships:GS ../data/upload/gene_snp.csv
--relationships:GA ../data/upload/snp_trait.csv
--relationships:MR ../data/upload/trait_trait.csv
the paper
the causal map of the human phenome: a first draft
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intro
- methods and data enable faster causal inference
- hypothesis driven analysis should use all methods to scrutinise
- we can precalculate these estimates but automation requires a number of things still
- instrument selection using steiger test
- method selection using linear discriminant analysis
- here we introduce a comprehensive analysis of 150 traits, introducing two ways for automating instrument selection and method selection
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results
- created graph
- steiger method simulations
- method selection simulations