eQTL analysis using methylation instead of SNPs - Githubissues

sr320 / ceabigr

Workshop on genomic data integration with a emphasis on epigenetic data (FHL 2022)

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eQTL analysis using methylation instead of SNPs #28

Open laurahspencer opened 2 years ago

laurahspencer commented 2 years ago

Laura taking lead. Data needs.

If investigating general relationship between methylation rate and expression:

Methylation status (methylated or not, locus-level) x individual matrix
Methylated loci location bedfile
Gene count (normalized) x individual matrix
Gene location bedfile

If investigating associations between DMLs (DMGs?) and DEGs identified among OA or sex factors:

DMLs OR DMGs x individual matrix
DMLs or DMGs location bedfile
DEGs count x individual matrix
DEG location bedfile

laurahspencer commented 2 years ago

Could also do a mQTL, would also need:

SNPs x individual matrix (filtered for ...?
SNPs location bedfile
% methylation x individual matrix
Methylation locations bedfile

Integrate somehow?

laurahspencer commented 2 years ago

Use R program MatrixEQTL