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allele_harmonise()
- allele_harmonise: Function to harmonize allele coding between a reference panel and GWAS/eQTL summary data
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build_LD_matrix()
- Build Blockwise Linkage Disequilibrium (LD) Matrix
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eQTLmapping_susie()
- eQTLmapping_susie: Function to perform eQTL fine-mapping using SuSiE and optional resampling
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filter_align()
- Filter and Align GWAS Data to a Reference Panel
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make_design_matrix()
- make_design_matrix: Constructs a Design Matrix of Z-scores for Gene-Tissue Pairs
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modified_predixcan()
- modified_predixcan: Function to estimate causal effects using a modified PrediXcan approach with BIC-based tuning parameter selection
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plot_tgvis()
- Plot GWAS Results with Credible-Set Annotation
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poet_shrinkage()
- poet_shrinkage: Function to perform covariance matrix shrinkage using the POET method
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R2_partition()
- R2_partition: Function to partition the Pratt index contributions of tissue-gene pairs, direct causal variants, and infinitesimal effects
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remove_missing_row_column()
- remove_missing_row_column: Removes Rows and Columns with Excessive Missing Values from a Matrix.
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tgvis()
- tgvis: Function to estimate and select the optimal number of single effects using profile-likelihood and BIC