Co-expression trans-eQTL analysis data

Sample metadata:

• sample_metadata.tsv - tab separated file with metadata for samples used in this analysis.

Gene expression matrix:

• Merged_ENSG_expression.tsv - integrated gene expression matrix used in the co-expression analysis (Ensembl IDs in rows and sample IDs in columns). The matrix can be split into sub matrices using the metadata from sample_metadata.tsv for separate analysis of cell types.

Genes in the modules:

• ICA_modules.tsv - data for assigning genes to modules from ICA method. Column 'loading' shows the contribution value of the gene to the module. Column 'approach' indicates if the module was detected from integrated or separate data. Column 'qtl_group' is an identifier for the cell type/condition.
• PEER_modules.tsv - data for assigning genes to modules from PEER method. Column 'loading' shows the contribution value of the gene to the module. 
• PLIER_modules.tsv - data for assigning genes to modules from PLIER method. Column 'loading' shows the contribution value of the gene to the module.
• WGCNA_modules.tsv - data for assigning genes to modules from WGCNA method. Column 'loading' shows the contribution value of the gene to the module. Column 'loading' has value 1 as the method assigns genes to modules without defining their contributions. 
• funcExplorer_modules.tsv - data for assigning genes to modules from funcExplorer method. Column 'loading' has value 1 as the method assigns genes to modules without defining their contributions. 

Module eigenvectors used for the trans-eQTL analysis

• eigenvectors_integrated.tsv - module eigenvectors for all the co-expression analysis methods applied to integrated data
• eigenvectors_separate.tsv- module eigenvectors for all the co-expression analysis methods applied to cell types separately

SuSiE fine mapping credible sets 

• SuSiE_credible_sets_integrated.tsv
• SuSiE_credible_sets_separate.tsv