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metabolomics_mdd

Code for analysis presented in the paper at : https://www.biologicalpsychiatryjournal.com/article/S0006-3223(23)00055-0/fulltext

https://github.com/elladavyson/metabolomics_mdd

Science Score: 67.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ✓
    CITATION.cff file
    Found CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ✓
    DOI references
    Found 2 DOI reference(s) in README
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    Academic publication links
    Links to: zenodo.org
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    Academic email domains
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    Institutional organization owner
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    JOSS paper metadata
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    Scientific vocabulary similarity
    Low similarity (6.0%) to scientific vocabulary
Last synced: 10 months ago · JSON representation ·

Repository

Code for analysis presented in the paper at : https://www.biologicalpsychiatryjournal.com/article/S0006-3223(23)00055-0/fulltext

Basic Info
  • Host: GitHub
  • Owner: Elladavyson
  • Language: R
  • Default Branch: main
  • Size: 54.7 KB
Statistics
  • Stars: 8
  • Watchers: 1
  • Forks: 2
  • Open Issues: 0
  • Releases: 1
Created over 3 years ago · Last pushed over 1 year ago
Metadata Files
Readme Citation

README.md

Metabolomic-investigation-of-major-depressive-disorder-identifies-a-potentially-causal-association-w

DOI

Code for analysis presented in the paper at : https://www.biologicalpsychiatryjournal.com/article/S0006-3223(23)00055-0/fulltext

Analysis Scripts

MetWAS

extractingQC.R - R script to extract spectrometer covariate from metabolite QC data metaboliteprocessingprelm.R - R script extracting the baseline metabolite data, normalising the metabolite data and merging with all covariates of interest UnadjustedMetWASlm.R - R script for the linear model looking at associations between each metabolite and MDD with base covariates AdjustedMetWAS_lm.R - R script for the linear model looking at associations between each metabolite and MDD with additional covariates

LD-score

LDscorescript - Bash script for running LD-score (ldsc) regression to find the heritability estimates for each metabolite rgmddmetabolitescript - Bash script for running LD-score (ldsc) regression to estimate the genetic correlation between MDD and metabolites readingrglogfilesmddmetabolite - Python script for reading the LD-score regression output files

MR

MetaboliteMDDMR.R - R script running the metabolite -> MDD MR analysis MRloopMDD_metabolite.R - R script running the MDD -> metabolite MR analysis

Colocalisation

SelecttopSNPperregionpermetaboliteellasversion.R - R script to go through the lead SNPs for each metabolite (in order of significance), and remove all SNPs within a 1Mb region to avoid running multiple of the same colocalisation tests (coloc kb distance = 1Mb) colocalisation_beginning - R script running colocalisation on metabolites (significant in MR analysis) and MDD

GTEx MR and colocalisation

GTExparquetdocu - R script documenting the extraction of GTEx data GTExMRinprog - R script for eQTLs (identified through GTEx data) -> MDD MR analysis colocalisationGTExfullsumstats.txt - R script for colocalisation analysis between GTEx eQTLs and MDD

Misc scripts (plots and functions)

functionsmetabolite.R - R script with common functions used throughout other scripts (getting metabolite names etc) locuszoom_meta.R - R script for making locus-zoom plots

Owner

  • Name: Ella Davyson
  • Login: Elladavyson
  • Kind: user

Citation (CITATION.cff) 

cff-version: 1.1.0
message: "If you use this code, please cite it as below."
authors:
  - family-names: Eleanor
    given-names: Davyson
    orcid: https://orcid.org/0000-0002-7313-0530
title: Elladavyson/Metabolomics_MDD: Metabolomics_MDD_UKB
version: 01
date-released: 2023-03-31

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